gromacs →
2020.5-4 →
armhf → 2021-02-12 02:13:10
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| gromacs 2020.5-4 (armhf) Thu, 11 Feb 2021 23:20:14 +0000 |
+==============================================================================+
Package: gromacs
Version: 2020.5-4
Source Version: 2020.5-4
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-e5f219e0-29d7-40dd-97b5-f7c5b79ca36d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.4 MB in 10s (2450 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 77.7 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gromacs 2020.5-4 (dsc) [2948 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gromacs 2020.5-4 (tar) [48.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main gromacs 2020.5-4 (tar) [29.1 MB]
Get:4 http://172.17.0.1/private bullseye-staging/main gromacs 2020.5-4 (diff) [38.3 kB]
Fetched 77.7 MB in 11s (7039 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-nTM2n0/gromacs-2020.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-nTM2n0' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-nPQSFt/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-nPQSFt/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-nPQSFt/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ Packages [435 B]
Fetched 2111 B in 0s (9795 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 9 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (63.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12563 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.4-5), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
Filtered Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.4-5), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-nPQSFt/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ Sources [585 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ Packages [671 B]
Fetched 2589 B in 0s (11.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext
gettext-base gfortran gfortran-10 groff-base hwloc-nox ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgfortran-10-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67
libjs-jquery libjs-jquery-ui libjsoncpp24 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3 libmpich-dev
libmpich12 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8
libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libslurm36
libssh2-1 libsub-override-perl libtool libuchardet0 libuv1 libx11-6
libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev
libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db media-types
mpich ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
po-debconf procps python3 python3-minimal python3.9 python3.9-minimal
x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make
gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-10-doc
libcoarrays-dev groff lrzip liblapack-doc libboost-doc libboost1.74-doc
libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev
libboost-context1.74-dev libboost-contract1.74-dev
libboost-coroutine1.74-dev libboost-date-time1.74-dev
libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libfftw3-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk
libx11-doc libxcb-doc m4-doc apparmor less www-browser mpich-doc opencl-icd
keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python3-doc
python3-tk python3-venv python3.9-venv python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
libgpm2 libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl
psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext
gettext-base gfortran gfortran-10 groff-base hwloc-nox ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgfortran-10-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67
libjs-jquery libjs-jquery-ui libjsoncpp24 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3 libmpich-dev
libmpich12 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8
libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libslurm36
libssh2-1 libsub-override-perl libtool libuchardet0 libuv1 libx11-6
libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev
libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db media-types
mpich ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
po-debconf procps python3 python3-minimal python3.9 python3.9-minimal
sbuild-build-depends-gromacs-dummy x11proto-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
0 upgraded, 131 newly installed, 0 to remove and 9 not upgraded.
Need to get 69.5 MB of archives.
After this operation, 391 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nPQSFt/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.1-4+rpi1 [790 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.1-4+rpi1 [1625 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.1-1 [37.8 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmpdec3 armhf 2.5.1-1+rpi1 [73.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.1-4+rpi1 [1615 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.1-4+rpi1 [465 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.1-1 [21.0 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.1-1 [64.1 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-2 [80.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libfido2-1 armhf 1.6.0-2 [47.2 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.4p1-3+b2 [793 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.18.4-2+rpi1 [1725 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.74.0-1 [305 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp24 armhf 1.9.4-4 [67.0 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.4.1-1 [140 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.40.0-1 [118 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.18.4-2+rpi1 [3118 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.3 [189 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182+20210205-1 [161 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.3 [1011 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf distro-info-data all 0.46 [7192 B]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-10-dev armhf 10.2.1-6+rpi1 [278 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf gfortran-10 armhf 10.2.1-6+rpi1 [7195 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:10.2.1-1+rpi1 [1428 B]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.4.1~rc2+dfsg-2 [122 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf hwloc-nox armhf 2.4.1~rc2+dfsg-2 [167 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 33.1-1 [51.7 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 33.1-1 [24.4 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libboost1.74-dev armhf 1.74.0-8 [9534 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf librdmacm1 armhf 33.1-1 [59.3 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.4.1~rc2+dfsg-2 [190 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.7.0-2 [310 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.7.0-2 [706 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libxnvctrl0 armhf 460.32.03-1 [25.6 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.9 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.4.1~rc2+dfsg-2 [19.9 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 33.1-1 [178 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libmpich12 armhf 3.4.1-3 [1530 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libslurm36 armhf 20.11.3-2 [587 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf mpich armhf 3.4.1-3 [188 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libmpich-dev armhf 3.4.1-3 [1893 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 4.0.0-4 [466 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.1.0-7+rpi1 [1768 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.1.0-7+rpi1 [177 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libpmix-dev armhf 4.0.0-4 [602 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.1.0-7+rpi1 [204 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.1.0-7+rpi1 [1142 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2020.1-1 [594 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.14-3 [171 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.7.0-2 [777 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf lsb-release all 11.1.0+rpi1 [28.1 kB]
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Setting up media-types (4.0.0) ...
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Setting up libboost1.74-dev:armhf (1.74.0-8) ...
Setting up libfftw3-single3:armhf (3.3.8-2) ...
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Setting up libbrotli1:armhf (1.0.9-2+b1) ...
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Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libpthread-stubs0-dev:armhf (0.4-1) ...
Setting up xtrans-dev (1.4.0-1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.40.0-1) ...
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
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Setting up libfftw3-double3:armhf (3.3.8-2) ...
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Setting up libjsoncpp24:armhf (1.9.4-4) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libnuma1:armhf (2.0.12-1) ...
Setting up libmd0:armhf (1.0.3-3) ...
Setting up libmpich12:armhf (3.4.1-3) ...
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Setting up libmpdec3:armhf (2.5.1-1+rpi1) ...
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Setting up libssh2-1:armhf (1.9.0-2) ...
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Setting up cmake-data (3.18.4-2+rpi1) ...
Setting up libboost-dev:armhf (1.74.0.3+b1) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Setting up libfido2-1:armhf (1.6.0-2) ...
Setting up libbsd0:armhf (0.11.3-1) ...
Setting up libelf1:armhf (0.182+20210205-1) ...
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Setting up libpython3.9-stdlib:armhf (3.9.1-4+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.1-1) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ...
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Setting up libxcb1:armhf (1.14-3) ...
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Setting up libedit2:armhf (3.1-20191231-2) ...
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Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnuma-dev:armhf (2.0.12-1) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-8) ...
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Setting up liblapack-dev:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up gfortran-10 (10.2.1-6+rpi1) ...
Setting up autoconf (2.69-14) ...
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Setting up dwz (0.13+20210201-1) ...
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Setting up groff-base (1.22.4-6) ...
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Setting up libcurl4:armhf (7.74.0-1) ...
Setting up libx11-6:armhf (2:1.7.0-2) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up python3.9 (3.9.1-4+rpi1) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up ibverbs-providers:armhf (33.1-1) ...
Setting up mpich (3.4.1-3) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/mpicc.1.gz because associated file /usr/share/man/man1/mpicc.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpic++.1.gz because associated file /usr/share/man/man1/mpicxx.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpicxx.1.gz because associated file /usr/share/man/man1/mpicxx.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpiCC.1.gz because associated file /usr/share/man/man1/mpicxx.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpif77.1.gz because associated file /usr/share/man/man1/mpif77.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpif90.1.gz because associated file /usr/share/man/man1/mpif90.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpifort.1.gz because associated file /usr/share/man/man1/mpifort.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/mpirun.1.gz because associated file /usr/share/man/man1/mpirun.mpich.1.gz (of link group mpirun) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.mpich.1.gz (of link group mpirun) doesn't exist
Setting up openssh-client (1:8.4p1-3+b2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libx11-dev:armhf (2:1.7.0-2) ...
Setting up libxext6:armhf (2:1.3.3-1.1) ...
Setting up python3 (3.9.1-1) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:10.2.1-1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libxnvctrl0:armhf (460.32.03-1) ...
Setting up dh-autoreconf (20) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-15) ...
Setting up libmpich-dev:armhf (3.4.1-3) ...
Setting up cmake (3.18.4-2+rpi1) ...
Setting up libhwloc-dev:armhf (2.4.1~rc2+dfsg-2) ...
Setting up lsb-release (11.1.0+rpi1) ...
Setting up librdmacm1:armhf (33.1-1) ...
Setting up debhelper (13.3.3) ...
Setting up libibverbs-dev:armhf (33.1-1) ...
Setting up libhwloc-plugins:armhf (2.4.1~rc2+dfsg-2) ...
Setting up libfabric1 (1.11.0-2) ...
Setting up libpmix2:armhf (4.0.0-4) ...
Setting up libopenmpi3:armhf (4.1.0-7+rpi1) ...
Setting up libpmix-dev:armhf (4.0.0-4) ...
Setting up openmpi-bin (4.1.0-7+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.1.0-7+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-9+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.9-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-6 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 chrpath_0.16-2 cmake_3.18.4-2+rpi1 cmake-data_3.18.4-2+rpi1 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.3 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.20-1 distro-info-data_0.46 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.45.7-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-6 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran_4:10.2.1-1+rpi1 gfortran-10_10.2.1-6+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hostname_3.23 hwloc-nox_2.4.1~rc2+dfsg-2 ibverbs-providers_33.1-1 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.18.3-4 libacl1_2.2.53-10 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36.1-6 libboost-dev_1.74.0.3+b1 libboost1.74-dev_1.74.0-8 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcbor0_0.5.0+dfsg-2 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.45.7-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libcurl4_7.74.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.3 libdpkg-perl_1.20.7.1+rpi1 libedit2_3.1-20191231-2 libelf1_0.182+20210205-1 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libexpat1_2.2.10-1 libext2fs2_1.45.7-1 libfabric1_1.11.0-2 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-6 libffi7_3.3-5 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.6.0-2 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran-10-dev_10.2.1-6+rpi1 libgfortran5_10.2.1-6+rpi1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libhwloc-dev_2.4.1~rc2+dfsg-2 libhwloc-plugins_2.4.1~rc2+dfsg-2 libhwloc15_2.4.1~rc2+dfsg-2 libibverbs-dev_33.1-1 libibverbs1_33.1-1 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 libjsoncpp24_1.9.4-4 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.57+dfsg-1 libldap-common_2.4.57+dfsg-1 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-1+rpi1 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.3-3 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpdec3_2.5.1-1+rpi1 libmpfr6_4.1.0-3 libmpich-dev_3.4.1-3 libmpich12_3.4.1-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.1.0-7+rpi1 libopenmpi3_4.1.0-7+rpi1 libp11-kit0_0.23.22-1 libpam-cap_1:2.44-1 libpam-modules_1.4.0-2 libpam-modules-bin_1.4.0-2 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpciaccess0_0.16-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-2 libpipeline1_1.5.3-1 libpmix-dev_4.0.0-4 libpmix2_4.0.0-4 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.9.1-1 libpython3.9-minimal_3.9.1-4+rpi1 libpython3.9-stdlib_3.9.1-4+rpi1 librdmacm1_33.1-1 libreadline8_8.1-1 librhash0_1.4.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libslurm36_20.11.3-2 libsmartcols1_2.36.1-6 libsqlite3-0_3.34.1-1 libss2_1.45.7-1 libssh2-1_1.9.0-2 libssl1.1_1.1.1i-3 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.2-5+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-6 libuv1_1.40.0-1 libx11-6_2:1.7.0-2 libx11-data_2:1.7.0-2 libx11-dev_2:1.7.0-2 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxcb1-dev_1.14-3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1.1 libxml2_2.9.10+dfsg-6.3 libxnvctrl0_460.32.03-1 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.9-1+rpi1 login_1:4.8.1-1 logsave_1.45.7-1 lsb-base_11.1.0+rpi1 lsb-release_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-6 mpich_3.4.1-3 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 ocl-icd-libopencl1_2.2.14-2 openmpi-bin_4.1.0-7+rpi1 openmpi-common_4.1.0-7+rpi1 openssh-client_1:8.4p1-3+b2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.32_5.32.1-2 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.16-5 python3_3.9.1-1 python3-minimal_3.9.1-1 python3.9_3.9.1-4+rpi1 python3.9-minimal_3.9.1-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2021a-1 util-linux_2.36.1-6 x11proto-dev_2020.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-1.0 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.K5NL0zCs/trustedkeys.kbx': General error
gpgv: Signature made Mon Feb 1 00:06:43 2021 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2020.5-4.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2020.5.orig.tar.gz
dpkg-source: info: unpacking gromacs_2020.5.orig-regressiontests.tar.gz
dpkg-source: info: unpacking gromacs_2020.5-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying disable-listed-forces-test.patch
dpkg-source: info: applying arm64-disable-numa-test.patch
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-e5f219e0-29d7-40dd-97b5-f7c5b79ca36d
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2020.5-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.5-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON)
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.5-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.5-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.mpich - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.mpich"
-- Using manually set library suffix: "_mpi.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.5-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.mpich - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.mpich"
-- Using manually set library suffix: "_mpi_d.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich-dp
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.5-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.openmpi"
-- Using manually set library suffix: "_mpi.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.5-4" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1rc2", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.openmpi"
-- Using manually set library suffix: "_mpi_d.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles /<<PKGBUILDDIR>>/build/basic//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 1%] Built target scanner
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2293 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../../lib/libgmxapi.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi.so.0.1.0 ../../../lib/libgmxapi.so.0 ../../../lib/libgmxapi.so
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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[ 0%] Built target release-version-info
Scanning dependencies of target thread_mpi
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
Scanning dependencies of target lmfit_objlib
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 1%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 1%] Built target scanner
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target thread_mpi
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
Scanning dependencies of target vmddlopen
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target vmddlopen
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:68:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
68 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target view_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 6%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
366 | put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box, atomsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::_ZN3gmx19StatePropagatorData24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target view_objlib
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 10%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1027:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1027 | fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1151:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1151 | fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1152 | bb_work_aligned);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:90:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
90 | nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 | { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | nullptr);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
259 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
263 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
267 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:99:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
99 | impl_->scale(coordinates);
| ~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:163:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
163 | impl_->transform(coordinates);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2293 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'int strip_dssp(FILE*, int, const gmx_bool*, real, real*, FILE*, t_matrix*, int*, const gmx_output_env_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In constructor 't_corr::t_corr(int, int, int, real, int, gmx_bool, gmx_bool, real, const t_topology*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'int gmx_nmtraj(int, char**)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:66:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
66 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:93:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:158:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
158 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:185:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_param(InteractionsOfType*, int, int, gmx::ArrayRef<const double>, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:55:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
55 | void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
64 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite4_atoms(InteractionsOfType*, int, int, int, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
101 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_atoms(InteractionsOfType*, int, int, int, int, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
90 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_cmap_param(InteractionsOfType*, int, int, int, int, int, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
70 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite2_param(InteractionsOfType*, int, int, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
77 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_param(InteractionsOfType*, int, int, int, int, real, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
84 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<InteractionOfType, int>}; _Tp = std::pair<InteractionOfType, int>; _Alloc = std::allocator<std::pair<InteractionOfType, int> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<InteractionOfType, int> >::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType>, gmx::ArrayRef<const InteractionOfType>, t_atoms*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
252 | static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1881 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_6ring(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, real, real, real, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1666 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_his(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void expand_hackblocks_one(const MoleculePatchDatabase&, std::string, std::vector<MoleculePatch>*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'void gen_pad(t_atoms*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<InteractionsOfType>, t_excls*, gmx::ArrayRef<MoleculePatchDatabase>, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
674 | ang.push_back(InteractionOfType(atomNumbers, {}, name));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:102: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
725 | dih.push_back(InteractionOfType(atomNumbers, {}, name));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:102: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:82: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
735 | dih.push_back(InteractionOfType(atoms, {}, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:82: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:90: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
754 | pai.push_back(InteractionOfType(atoms, {}, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:90: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
847 | dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
889 | rtpFFDB[0].bRemoveDihedralIfWithImproper);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
389 | improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_trp(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_tyr(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'void do_vsites(gmx::ArrayRef<const PreprocessResidue>, PreprocessingAtomTypes*, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, gmx::ArrayRef<InteractionsOfType>, int**, int**, real, bool, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:101: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2247 | *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:101: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&, char**, const InteractionOfType&, int&, int&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'int PreprocessingAtomTypes::addType(t_symtab*, const t_atom&, const string&, const InteractionOfType&, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/streambuf:41,
from /usr/include/c++/10/bits/streambuf_iterator.h:35,
from /usr/include/c++/10/iterator:66,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AtomTypeData&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/streambuf:41,
from /usr/include/c++/10/bits/streambuf_iterator.h:35,
from /usr/include/c++/10/iterator:66,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/ext/new_allocator.h: In member function 'void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType>, gmx_mtop_t*, int*, bool)':
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void copyPreprocessResidues(const PreprocessResidue&, PreprocessResidue*, t_symtab*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp: In constructor 'InteractionOfType::InteractionOfType(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const string&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp:111:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
111 | InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void mergeAtomModifications(const MoleculePatchDatabase&, MoleculePatchDatabase*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In function 'void insert_mols(int, int, int, real, real, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, const std::set<int>&, const t_atoms&, gmx::ArrayRef<gmx::BasicVector<double> >, int, real (*)[3], const string&, const real*, RotationType)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:166:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | static void insert_mols(int nmol_insrt,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, AtomProperties*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In member function 'virtual int gmx::{anonymous}::InsertMolecules::run()':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:584:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
584 | insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_, &atoms, &top_.symtab,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
585 | &x_, removableAtoms, atomsInserted, xInserted, ePBCForOutput, box_, positionFile_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | deltaR_, enumRot_);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp: In function 'int nm2type(int, t_nm2type*, t_symtab*, t_atoms*, PreprocessingAtomTypes*, int*, InteractionsOfType*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
342 | k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void read_h_db_file(const char*, std::vector<MoleculePatchDatabase>*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void add_atom_to_restp(PreprocessResidue*, t_symtab*, int, const MoleculePatch*)':
/usr/include/c++/10/bits/vector.tcc:161:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, t_atoms*, t_symtab*, gmx::ArrayRef<gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:1305:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1305 | void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:553:53: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
553 | bool groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
554 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:584:52: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
584 | groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
585 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'void sort_pdbatoms(gmx::ArrayRef<const PreprocessResidue>, int, t_atoms**, t_atoms**, std::vector<gmx::BasicVector<double> >*, t_blocka*, char***)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1666 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void pdb2top(FILE*, const char*, const char*, t_atoms*, std::vector<gmx::BasicVector<double> >*, PreprocessingAtomTypes*, t_symtab*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, bool, bool, bool, const char*, real, gmx::ArrayRef<const DisulfideBond>, real, real, bool, bool, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
782 | add_param(psb, ai, aj, {}, patch.s.c_str());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
796 | add_param(psb, i, i + 1, {}, nullptr); /* C-O */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
797 | add_param(psb, i, i + 2, {}, nullptr); /* C-OA */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
798 | add_param(psb, i + 2, i + 3, {}, nullptr); /* OA-H */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
803 | add_param(psb, i, i + k + 1, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
729 | add_param(ps, ai, aj, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual int gmx::{anonymous}::pdb2gmx::run()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:2149:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2149 | match_atomnames_with_rtp(restp_chain, hb_chain, pdba, &symtab, x, bVerbose_);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp: In function 'PreprocessingAtomTypes read_atype(const char*, t_symtab*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | at.addType(tab, *a, name, InteractionOfType({}, {}), 0, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SpecialBond&}; _Tp = SpecialBond; _Alloc = std::allocator<SpecialBond>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SpecialBond>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void readResidueDatabase(const string&, std::vector<PreprocessResidue>*, PreprocessingAtomTypes*, t_symtab*, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<SpecialBond> generateSpecialBonds()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void read_ter_db_file(const char*, std::vector<MoleculePatchDatabase>*, PreprocessingAtomTypes*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp: In function 'void convert_harmonics(gmx::ArrayRef<MoleculeInformation>, PreprocessingAtomTypes*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
231 | InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp: In function 'void make_shake(gmx::ArrayRef<InteractionsOfType>, t_atoms*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | InteractionOfType(atomNumbers, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
194 | add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp: In function 'void print_bondeds(FILE*, int, Directive, int, int, gmx::ArrayRef<const InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
340 | atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void add_param_to_list(InteractionsOfType*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp: In function 'char** read_topol(const char*, const char*, const char*, const char*, t_symtab*, PreprocessingAtomTypes*, std::vector<MoleculeInformation>*, std::unique_ptr<MoleculeInformation>*, gmx::ArrayRef<InteractionsOfType>, int*, double*, t_gromppopts*, real*, std::vector<gmx_molblock_t>*, bool*, bool, bool, bool, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
135 | pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_LJCpairsNB(MoleculeInformation*, int, InteractionsOfType*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:106: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2658 | add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:106: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_at(t_symtab*, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, int, t_nbparam***, t_nbparam***, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
541 | InteractionOfType interactionType({}, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite3_param(PreprocessingAtomTypes*, InteractionOfType*, t_atoms*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:402:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
402 | static bool calc_vsite3_param(PreprocessingAtomTypes* atypes,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:402:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_vsitesn(Directive, gmx::ArrayRef<InteractionsOfType>, t_atoms*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2443 | add_param_to_list(&bond[ftype], InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'int add_atomtype_decoupled(t_symtab*, PreprocessingAtomTypes*, t_nbparam***, t_nbparam***)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2574 | nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VsiteBondedInteraction}; _Tp = VsiteBondedInteraction; _Alloc = std::allocator<VsiteBondedInteraction>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VsiteBondedInteraction>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bond(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, bool, bool, real, bool, bool*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1984 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void enter_bonded(int, std::vector<VsiteBondedInteraction>*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'void lo_set_force_const(InteractionsOfType*, real*, int, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'int set_vsites(bool, t_atoms*, PreprocessingAtomTypes*, gmx::ArrayRef<InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
821 | bERROR = calc_vsite3_param(atypes, ¶m, atoms, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
822 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_cmap(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2336 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'int gmx_x2top(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
137 | add_param_to_list(bond, InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_nbparams(int, int, InteractionsOfType*, PreprocessingAtomTypes*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
127 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
151 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:97: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
184 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:97: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bondtype(InteractionsOfType*, const InteractionOfType&, int, int, bool, const char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
711 | InteractionOfType(b.atoms(), b.forceParam(), b.interactionTypeName()));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
730 | bt->interactionTypes.emplace_back(InteractionOfType(atoms, forceParam, b.interactionTypeName()));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bt(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
851 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_dihedraltype(Directive, gmx::ArrayRef<InteractionsOfType>, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1019 | push_bondtype(&(bt[ftype]), InteractionOfType(atoms, forceParam), 4, ftype, bAllowRepeat, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void push_cmaptype(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1286 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void convert_pairs_to_pairsQ(gmx::ArrayRef<InteractionsOfType>, real, t_atoms*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2606 | paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType>, int, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:583:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
583 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
714 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
715 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1245 | put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box, positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:400:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
400 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/10/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
708 | lincs_update_atoms(lincsd, th, 1.0, sol, r,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
709 | (econq != ConstraintVariable::Force) ? invmass : nullptr, fp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1079:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1079 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1141:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1141 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1590 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1601:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1601 | stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1602 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1613:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1613 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1634:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1634 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1771:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1771 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1790:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1790 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
56 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:143:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
144 | state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::Update*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1752:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1752 | upd->deform()->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1868:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1868 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1896 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->sd()->randomize_group, upd->sd()->boltzfac);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function 'gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:338:26: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
338 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
741 | void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, int, double, const gmx::DensityFittingForceProviderState&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:79:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
79 | scaleToLattice({ &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:166:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
167 | { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:171:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:172:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
172 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:210:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
210 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:258:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
258 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:551:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:896:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
896 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1035:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1035 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1036 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
952 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:711:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
728 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
730 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
731 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
732 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
733 | &dvdlambda_lj, pmeFlags);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1004 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1384 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1393 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:379:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
379 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:421:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
421 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
422 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
424 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:437:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
437 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
438 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
439 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:451:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
451 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
452 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
453 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:509:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
509 | dd_collect_vec(cr->dd, state, flocal, ftemp);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:519:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
519 | mimicCommunicator.sendForces(ftemp, state_global->natoms);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:533:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
533 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:845:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
845 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
846 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
847 | ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ems->s.lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
848 | graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:905:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
905 | sum_dhdl(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:749:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
749 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:753:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
753 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
754 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
755 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:767:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
767 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:810:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:815:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
815 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:918:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
918 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
919 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
920 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
921 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
922 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:945:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
945 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
946 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
947 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
948 | fr, runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
949 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1100:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1100 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1128:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1128 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1136:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1136 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1152:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1152 | stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1159:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1159 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1161 | checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1162 | mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1194:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1194 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1266:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1266 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1267:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1267 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1273:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1273 | stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1290:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1290 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1393:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1393 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1429:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1429 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1437:58: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1437 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1455:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1455 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, PaddedHostVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:385:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
385 | initialize_lambdas(fplog, *ir, MASTER(cr), &(state_global->fep_state), state_global->lambda, nullptr);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1858:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1858 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1859 | static_cast<real>(step), &ems.s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1860 | observablesHistory, ems.f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
302 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:551:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
551 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
556 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:567:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
567 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
568 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:581:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
581 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
582 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:641:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
641 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2766:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2766 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2767 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2768 | fcd, state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2769 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2770 | state_work.s.lambda, &state_work.s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2771 | state_work.f.arrayRefWithPadding(), vir, mdatoms, nrnb,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2772 | wcycle, graph, shellfc, fr, runScheduleWork, t, mu_tot,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2773 | vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, const gmx_vsite_t*, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:936:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
936 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1094:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1094 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1095 | nrnb, wcycle, top, box, x, hist, forceWithPadding[Min], force_vir, md, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1096 | lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1097 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1188:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1188 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1189 | wcycle, top, box, posWithPadding[Try], hist, forceWithPadding[Try], force_vir, md,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1190 | enerd, fcd, lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1191 | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::LegacySimulator::do_tpi()':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:591:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
591 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:663:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
663 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
664 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
722 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:745:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
745 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
746 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
747 | &state_global->hist, f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
748 | state_global->lambda, nullptr, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
749 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
750 | DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'int gmx::Mdrunner::mdrunner()':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1395:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1395 | constructVsitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:132:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
132 | void StatePropagatorDataGpu::copyCoordinatesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:147:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
147 | void StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:164:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
164 | void StatePropagatorDataGpu::copyVelocitiesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:180:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
180 | void StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:204:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
204 | void StatePropagatorDataGpu::copyForcesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
229 | void StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:271:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
271 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 'void writeXpmAxis(FILE*, const char*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:809:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | static void writeXpmAxis(FILE* out, const char* axis, ArrayRef<const real> label)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<t_matrix> read_xpm_matrix(const char*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.5.0.0 ../../lib/libgromacs_d.so.5 ../../lib/libgromacs_d.so
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[ 98%] Built target libgromacs
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
Scanning dependencies of target gmx
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
Scanning dependencies of target gmxapi
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../../lib/libgmxapi_d.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi_d.so.0.1.0 ../../../lib/libgmxapi_d.so.0 ../../../lib/libgmxapi_d.so
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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils /<<PKGBUILDDIR>>/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target testutils-test
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target domdec-test
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target fft-test
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 72%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target gpu_utils-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target math-test
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target random-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target options-test
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target gmxana-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target simd-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx1-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
Scanning dependencies of target coordinateio-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target energyanalysis-test
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target gmxpreprocess-test
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-modules-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target fileio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target mdrun-modules-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
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Scanning dependencies of target mdrun-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/dispersion_correction.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-output-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
[ 90%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target mdrun-io-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target gmxapi-mpi-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target gmxapi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target workflow-details-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (16 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (25 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (1 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (1 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (1 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (5 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (47 ms total)
1: [ PASSED ] 59 tests.
1/54 Test #1: TestUtilsUnitTests .................. Passed 0.07 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (1 ms)
2: [----------] 1 test from MpiSelfTest (1 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (1 ms total)
2: [ PASSED ] 1 test.
2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.02 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 347 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (0 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (1 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (1 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 4 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 4 tests from EnumerationHelpersTest (1 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (0 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
3: [----------] 6 tests from TreeValueTransformTest (2 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (0 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (1 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
3: [----------] 7 tests from LoggerTest (4 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (0 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (0 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (1 ms)
3: [----------] 2 tests from PathTest (1 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (1 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (2 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (1 ms)
3: [----------] 2 tests from FormatStringTest (1 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (0 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
3: [----------] 10 tests from TextLineWrapperTest (2 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (1 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (0 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
3: [----------] 6 tests from TextWriterTest (1 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (1 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (1 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (2 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 347 tests from 56 test cases ran. (35 ms total)
3: [ PASSED ] 347 tests.
3/54 Test #3: UtilityUnitTests .................... Passed 0.09 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (2 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (2 ms total)
4: [ PASSED ] 2 tests.
4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.02 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 187 tests from 13 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (1 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms)
5: [----------] 2 tests from PrEbinTest (2 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
5: [----------] 4 tests from ShakeTest (0 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (0 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (1 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (0 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (0 ms)
5: [----------] 9 tests from UpdateGroups (1 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms)
5: [----------] 1 test from UpdateGroupsCog (1 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (11 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (5 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (7 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (1 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (24 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (7 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (7 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (7 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (96 ms total)
5:
5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (1 ms total)
5:
5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (1 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (8 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (3 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (38 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (2 ms)
5: [----------] 13 tests from WithParameters/SettleTest (15 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 187 tests from 13 test cases ran. (167 ms total)
5: [ PASSED ] 187 tests.
5/54 Test #5: MdlibUnitTest ....................... Passed 0.20 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (0 ms)
6: [----------] 2 tests from DensityFittingTest (2 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (2 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (0 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (0 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (1 ms)
6: [----------] 3 tests from ElectricFieldTest (1 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (5 ms total)
6: [ PASSED ] 20 tests.
6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.02 sec
test 7
Start 7: CommandLineUnitTests
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 59 tests from 7 test cases.
7: [----------] Global test environment set-up.
7: [----------] 3 tests from CommandLineHelpModuleTest
7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (2 ms)
7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms)
7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (3 ms)
7: [----------] 3 tests from CommandLineHelpModuleTest (5 ms total)
7:
7: [----------] 7 tests from CommandLineHelpWriterTest
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
7: [----------] 7 tests from CommandLineHelpWriterTest (4 ms total)
7:
7: [----------] 6 tests from CommandLineModuleManagerTest
7: [ RUN ] CommandLineModuleManagerTest.RunsModule
7: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
7: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total)
7:
7: [----------] 13 tests from CommandLineParserTest
7: [ RUN ] CommandLineParserTest.HandlesSingleValues
7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesString
7: [ OK ] CommandLineParserTest.HandlesString (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (1 ms)
7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
7: [----------] 13 tests from CommandLineParserTest (2 ms total)
7:
7: [----------] 6 tests from CommandLineProgramContextTest
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms)
7: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
7:
7: [----------] 3 tests from OutputNamesTest
7: [ RUN ] OutputNamesTest.CanBeSuffixed
7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
7: [----------] 3 tests from OutputNamesTest (0 ms total)
7:
7: [----------] 21 tests from ParseCommonArgsTest
7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms)
7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
7: [----------] 21 tests from ParseCommonArgsTest (7 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 59 tests from 7 test cases ran. (22 ms total)
7: [ PASSED ] 59 tests.
7/54 Test #7: CommandLineUnitTests ................ Passed 0.04 sec
test 8
Start 8: DomDecTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 9 tests from 2 test cases.
8: [----------] Global test environment set-up.
8: [----------] 7 tests from HashedMap
8: [ RUN ] HashedMap.InsertsFinds
8: [ OK ] HashedMap.InsertsFinds (0 ms)
8: [ RUN ] HashedMap.NegativeKeysWork
8: [ OK ] HashedMap.NegativeKeysWork (0 ms)
8: [ RUN ] HashedMap.InsertsErases
8: [ OK ] HashedMap.InsertsErases (0 ms)
8: [ RUN ] HashedMap.InsertsOrAssigns
8: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
8: [ RUN ] HashedMap.Clears
8: [ OK ] HashedMap.Clears (0 ms)
8: [ RUN ] HashedMap.LinkedEntries
8: [ OK ] HashedMap.LinkedEntries (0 ms)
8: [ RUN ] HashedMap.ResizesTable
8: [ OK ] HashedMap.ResizesTable (0 ms)
8: [----------] 7 tests from HashedMap (1 ms total)
8:
8: [----------] 2 tests from LocalAtomSetManager
8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
8: [----------] 2 tests from LocalAtomSetManager (0 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 9 tests from 2 test cases ran. (1 ms total)
8: [ PASSED ] 9 tests.
8/54 Test #8: DomDecTests ......................... Passed 0.02 sec
test 9
Start 9: EwaldUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 257 tests from 10 test cases.
9: [----------] Global test environment set-up.
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (6 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (7 ms total)
9:
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (11 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (4 ms)
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (114 ms total)
9:
9: [----------] 144 tests from SaneInput/PmeGatherTest
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms)
9: [----------] 144 tests from SaneInput/PmeGatherTest (141 ms total)
9:
9: [----------] 16 tests from SaneInput/PmeSolveTest
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (5 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (3 ms)
9: [----------] 16 tests from SaneInput/PmeSolveTest (47 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms)
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (16 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (29 ms total)
9:
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (2 ms)
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (45 ms total)
9:
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (6 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (6 ms)
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (52 ms total)
9:
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms)
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (68 ms total)
9:
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (13 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (15 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (20 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (22 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (9 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (10 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (13 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (14 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (18 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (21 ms)
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (209 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 257 tests from 10 test cases ran. (752 ms total)
9: [ PASSED ] 257 tests.
9/54 Test #9: EwaldUnitTests ...................... Passed 0.84 sec
test 10
Start 10: FFTUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 14 tests from 4 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from ManyFFTTest
10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (8 ms)
10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (13 ms)
10: [----------] 2 tests from ManyFFTTest (23 ms total)
10:
10: [----------] 1 test from FFTTest
10: [ RUN ] FFTTest.Real2DLength18_15Test
10: [ OK ] FFTTest.Real2DLength18_15Test (5 ms)
10: [----------] 1 test from FFTTest (5 ms total)
10:
10: [----------] 1 test from FFFTest3D
10: [ RUN ] FFFTest3D.Real5_6_9
10: [ OK ] FFFTest3D.Real5_6_9 (3 ms)
10: [----------] 1 test from FFFTest3D (3 ms total)
10:
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (8 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (12 ms)
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (32 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 14 tests from 4 test cases ran. (63 ms total)
10: [ PASSED ] 14 tests.
10/54 Test #10: FFTUnitTests ........................ Passed 0.08 sec
test 11
Start 11: GpuUtilsUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 62 tests from 20 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ClfftInitializer
11: [ RUN ] ClfftInitializer.SingleInitializationWorks
11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
11: [ RUN ] ClfftInitializer.TwoInitializationsWork
11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
11: [----------] 2 tests from ClfftInitializer (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Swap
11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Comparison
11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Swap
11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Comparison
11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Swap
11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Comparison
11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Swap
11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Comparison
11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/3 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
11:
11: [----------] 1 test from HostAllocatorUntypedTest
11: [ RUN ] HostAllocatorUntypedTest.Comparison
11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/0.Move
11: [ OK ] AllocatorTest/0.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/0 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.Move
11: [ OK ] AllocatorTest/1.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/1 (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.Move
11: [ OK ] AllocatorTest/2.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/2 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.Move
11: [ OK ] AllocatorTest/3.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/3 (0 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 62 tests from 20 test cases ran. (5 ms total)
11: [ PASSED ] 62 tests.
11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.03 sec
test 12
Start 12: HardwareUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 4 tests from 1 test case.
12: [----------] Global test environment set-up.
12: [----------] 4 tests from HardwareTopologyTest
12: [ RUN ] HardwareTopologyTest.Execute
12: [ OK ] HardwareTopologyTest.Execute (18 ms)
12: [ RUN ] HardwareTopologyTest.HwlocExecute
12: [ OK ] HardwareTopologyTest.HwlocExecute (17 ms)
12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (18 ms)
12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (17 ms)
12: [----------] 4 tests from HardwareTopologyTest (70 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 4 tests from 1 test case ran. (70 ms total)
12: [ PASSED ] 4 tests.
12/54 Test #12: HardwareUnitTests ................... Passed 0.09 sec
test 13
Start 13: MathUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 204 tests from 29 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from EmptyArrayRefWithPaddingTest
13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
13:
13: [----------] 8 tests from TranslateAndScaleTest
13: [ RUN ] TranslateAndScaleTest.identityTransformation
13: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingIdentity
13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (1 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
13: [----------] 8 tests from TranslateAndScaleTest (2 ms total)
13:
13: [----------] 12 tests from DensitySimilarityTest
13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (60 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (60 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (137 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms)
13: [----------] 12 tests from DensitySimilarityTest (259 ms total)
13:
13: [----------] 6 tests from StructureSimilarityTest
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
13: [----------] 6 tests from StructureSimilarityTest (0 ms total)
13:
13: [----------] 8 tests from ExponentialMovingAverage
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
13: [----------] 8 tests from ExponentialMovingAverage (0 ms total)
13:
13: [----------] 21 tests from FunctionTest
13: [ RUN ] FunctionTest.StaticLog2
13: [ OK ] FunctionTest.StaticLog2 (0 ms)
13: [ RUN ] FunctionTest.Log2I32Bit
13: [ OK ] FunctionTest.Log2I32Bit (0 ms)
13: [ RUN ] FunctionTest.Log2I64Bit
13: [ OK ] FunctionTest.Log2I64Bit (0 ms)
13: [ RUN ] FunctionTest.GreatestCommonDivisor
13: [ OK ] FunctionTest.GreatestCommonDivisor (1 ms)
13: [ RUN ] FunctionTest.InvsqrtFloat
13: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvsqrtDouble
13: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvsqrtInteger
13: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
13: [ RUN ] FunctionTest.InvcbrtFloat
13: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvcbrtDouble
13: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvcbrtInteger
13: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
13: [ RUN ] FunctionTest.SixthrootFloat
13: [ OK ] FunctionTest.SixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.SixthrootDouble
13: [ OK ] FunctionTest.SixthrootDouble (0 ms)
13: [ RUN ] FunctionTest.SixthrootInteger
13: [ OK ] FunctionTest.SixthrootInteger (1 ms)
13: [ RUN ] FunctionTest.InvsixthrootFloat
13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootDouble
13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootInteger
13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
13: [ RUN ] FunctionTest.Powers
13: [ OK ] FunctionTest.Powers (0 ms)
13: [ RUN ] FunctionTest.ErfInvFloat
13: [ OK ] FunctionTest.ErfInvFloat (0 ms)
13: [ RUN ] FunctionTest.ErfInvDouble
13: [ OK ] FunctionTest.ErfInvDouble (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
13: [----------] 21 tests from FunctionTest (6 ms total)
13:
13: [----------] 4 tests from GaussianOn1DLattice
13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
13: [ RUN ] GaussianOn1DLattice.isCorrect
13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
13: [----------] 4 tests from GaussianOn1DLattice (0 ms total)
13:
13: [----------] 9 tests from GaussTransformTest
13: [ RUN ] GaussTransformTest.isZeroUponConstruction
13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
13: [ RUN ] GaussTransformTest.view
13: [ OK ] GaussTransformTest.view (0 ms)
13: [----------] 9 tests from GaussTransformTest (1 ms total)
13:
13: [----------] 3 tests from DensityFittingForce
13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
13: [ RUN ] DensityFittingForce.pullsTowardsDerivative
13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
13: [----------] 3 tests from DensityFittingForce (1 ms total)
13:
13: [----------] 2 tests from InvertMatrixTest
13: [ RUN ] InvertMatrixTest.IdentityIsImpotent
13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertMatrixTest.ComputesInverse
13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
13: [----------] 2 tests from InvertMatrixTest (0 ms total)
13:
13: [----------] 2 tests from InvertBoxMatrixTest
13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
13:
13: [----------] 15 tests from MatrixTest
13: [ RUN ] MatrixTest.canSetFromArray
13: [ OK ] MatrixTest.canSetFromArray (0 ms)
13: [ RUN ] MatrixTest.canSetStaticallyFromList
13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
13: [ RUN ] MatrixTest.canConstructAndFill
13: [ OK ] MatrixTest.canConstructAndFill (0 ms)
13: [ RUN ] MatrixTest.canSetValues
13: [ OK ] MatrixTest.canSetValues (0 ms)
13: [ RUN ] MatrixTest.canCopyAssign
13: [ OK ] MatrixTest.canCopyAssign (0 ms)
13: [ RUN ] MatrixTest.canSwap
13: [ OK ] MatrixTest.canSwap (0 ms)
13: [ RUN ] MatrixTest.staticMultiDimArrayExtent
13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MatrixTest.determinantWorks
13: [ OK ] MatrixTest.determinantWorks (0 ms)
13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
13: [ RUN ] MatrixTest.traceWorks
13: [ OK ] MatrixTest.traceWorks (0 ms)
13: [ RUN ] MatrixTest.transposeWorks
13: [ OK ] MatrixTest.transposeWorks (1 ms)
13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
13: [ RUN ] MatrixTest.canFillLegacyMatrix
13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
13: [----------] 15 tests from MatrixTest (1 ms total)
13:
13: [----------] 25 tests from MultiDimArrayTest
13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapStatic
13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapDynamic
13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToView
13: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToConstView
13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
13: [ RUN ] MultiDimArrayTest.viewBegin
13: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.viewEnd
13: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstBegin
13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstEnd
13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
13: [----------] 25 tests from MultiDimArrayTest (1 ms total)
13:
13: [----------] 4 tests from MultiDimArrayToMdSpanTest
13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanCopyAssign
13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanMoveAssign
13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanSwap
13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanCopyAssign
13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanMoveAssign
13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanSwap
13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/1 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanCopyAssign
13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanMoveAssign
13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanSwap
13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanCopyAssign
13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanMoveAssign
13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanSwap
13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanCopyAssign
13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanMoveAssign
13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanSwap
13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanCopyAssign
13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanMoveAssign
13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanSwap
13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/5 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanCopyAssign
13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanMoveAssign
13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanSwap
13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanCopyAssign
13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanMoveAssign
13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanSwap
13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanCopyAssign
13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanMoveAssign
13: [ OK ] PaddedVectorTest/8.CanMoveAssign (1 ms)
13: [ RUN ] PaddedVectorTest/8.CanSwap
13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/8 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanCopyAssign
13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanMoveAssign
13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanSwap
13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
13:
13: [----------] 37 tests from RVecTest
13: [ RUN ] RVecTest.CanBeStoredInVector
13: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAsMutable_rvec
13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Array
13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
13: [ RUN ] RVecTest.CanAddRVecToRvec
13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanAddAssignRVecToRvec
13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractRVecFromRvec
13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanDotProductRVecByRvec
13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanCrossProductRVecByRvec
13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVecInplace
13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
13: [ RUN ] RVecTest.CanScaleRVec
13: [ OK ] RVecTest.CanScaleRVec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVec
13: [ OK ] RVecTest.CanDivideRVec (0 ms)
13: [ RUN ] RVecTest.CanDoUnitvFromRVec
13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanSqLengthOfRVec
13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanLengthOfRVec
13: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToRVec
13: [ OK ] RVecTest.CanCastToRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToDVec
13: [ OK ] RVecTest.CanCastToDVec (0 ms)
13: [ RUN ] RVecTest.CanLeftScalarMultiply
13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanRightScalarMultiply
13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanGetUnitvFromRVec
13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanGetSqLengthOfRVec
13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanGetLengthOfRVec
13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoCrossProductOfRVec
13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoDotProductOfRVec
13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanScaleByVector
13: [ OK ] RVecTest.CanScaleByVector (0 ms)
13: [ RUN ] RVecTest.asIVec
13: [ OK ] RVecTest.asIVec (0 ms)
13: [ RUN ] RVecTest.elementWiseMin
13: [ OK ] RVecTest.elementWiseMin (0 ms)
13: [ RUN ] RVecTest.elementWiseMax
13: [ OK ] RVecTest.elementWiseMax (0 ms)
13: [ RUN ] RVecTest.WorksAs_dvec_Reference
13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_ivec_Reference
13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Reference
13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
13: [ RUN ] RVecTest.CopyConstructorWorks
13: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
13: [ RUN ] RVecTest.CopyAssignmentWorks
13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
13: [ RUN ] RVecTest.MoveConstructorWorks
13: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
13: [ RUN ] RVecTest.MoveAssignmentWorks
13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
13: [----------] 37 tests from RVecTest (1 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 204 tests from 29 test cases ran. (276 ms total)
13: [ PASSED ] 204 tests.
13/54 Test #13: MathUnitTests ....................... Passed 0.31 sec
test 14
Start 14: MdrunUtilityUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 17 tests from 1 test case.
14: [----------] Global test environment set-up.
14: [----------] 17 tests from ThreadAffinityTest
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
14: NOTE: Affinity setting failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
14: NOTE: Affinity setting for 1/2 threads failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (3 ms)
14: [----------] 17 tests from ThreadAffinityTest (15 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 17 tests from 1 test case ran. (15 ms total)
14: [ PASSED ] 17 tests.
14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.04 sec
test 15
Start 15: MdrunUtilityMpiUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 13 tests from 2 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from ThreadAffinityMultiRankTest
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (6 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (7 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (5 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (7 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
15: [----------] 6 tests from ThreadAffinityMultiRankTest (30 ms total)
15:
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (6 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (6 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (7 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (5 ms)
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (37 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 13 tests from 2 test cases ran. (67 ms total)
15: [ PASSED ] 13 tests.
15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 0.09 sec
test 16
Start 16: MDSpanTests
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MDSpanTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 32 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 4 tests from BasicAccessorPolicy
16: [ RUN ] BasicAccessorPolicy.Decay
16: [ OK ] BasicAccessorPolicy.Decay (0 ms)
16: [ RUN ] BasicAccessorPolicy.Access
16: [ OK ] BasicAccessorPolicy.Access (0 ms)
16: [ RUN ] BasicAccessorPolicy.Offset
16: [ OK ] BasicAccessorPolicy.Offset (0 ms)
16: [ RUN ] BasicAccessorPolicy.CopyAccessor
16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
16: [----------] 4 tests from BasicAccessorPolicy (0 ms total)
16:
16: [----------] 4 tests from ExtentsTest
16: [ RUN ] ExtentsTest.Construction
16: [ OK ] ExtentsTest.Construction (0 ms)
16: [ RUN ] ExtentsTest.PurelyStatic
16: [ OK ] ExtentsTest.PurelyStatic (0 ms)
16: [ RUN ] ExtentsTest.RankNought
16: [ OK ] ExtentsTest.RankNought (0 ms)
16: [ RUN ] ExtentsTest.Assignment
16: [ OK ] ExtentsTest.Assignment (0 ms)
16: [----------] 4 tests from ExtentsTest (0 ms total)
16:
16: [----------] 8 tests from MdSpanExtension
16: [ RUN ] MdSpanExtension.SlicingAllStatic
16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingDynamic
16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingAllStatic3D
16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
16: [ RUN ] MdSpanExtension.SlicingEqualsView3D
16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
16: [ RUN ] MdSpanExtension.additionWorks
16: [ OK ] MdSpanExtension.additionWorks (0 ms)
16: [ RUN ] MdSpanExtension.subtractionWorks
16: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
16: [ RUN ] MdSpanExtension.multiplicationWorks
16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
16: [ RUN ] MdSpanExtension.divisionWorks
16: [ OK ] MdSpanExtension.divisionWorks (0 ms)
16: [----------] 8 tests from MdSpanExtension (0 ms total)
16:
16: [----------] 3 tests from LayoutTests
16: [ RUN ] LayoutTests.LayoutRightConstruction
16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
16: [ RUN ] LayoutTests.LayoutRightProperties
16: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
16: [ RUN ] LayoutTests.LayoutRightOperator
16: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
16: [----------] 3 tests from LayoutTests (1 ms total)
16:
16: [----------] 1 test from MdSpanTest
16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
16: [----------] 1 test from MdSpanTest (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
16: [ RUN ] MdSpanTest/0.Rank
16: [ OK ] MdSpanTest/0.Rank (0 ms)
16: [ RUN ] MdSpanTest/0.DynamicRank
16: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/0.Extents
16: [ OK ] MdSpanTest/0.Extents (0 ms)
16: [ RUN ] MdSpanTest/0.Strides
16: [ OK ] MdSpanTest/0.Strides (0 ms)
16: [ RUN ] MdSpanTest/0.Properties
16: [ OK ] MdSpanTest/0.Properties (0 ms)
16: [ RUN ] MdSpanTest/0.Operator
16: [ OK ] MdSpanTest/0.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/0 (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
16: [ RUN ] MdSpanTest/1.Rank
16: [ OK ] MdSpanTest/1.Rank (0 ms)
16: [ RUN ] MdSpanTest/1.DynamicRank
16: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/1.Extents
16: [ OK ] MdSpanTest/1.Extents (0 ms)
16: [ RUN ] MdSpanTest/1.Strides
16: [ OK ] MdSpanTest/1.Strides (0 ms)
16: [ RUN ] MdSpanTest/1.Properties
16: [ OK ] MdSpanTest/1.Properties (0 ms)
16: [ RUN ] MdSpanTest/1.Operator
16: [ OK ] MdSpanTest/1.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/1 (0 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 32 tests from 7 test cases ran. (2 ms total)
16: [ PASSED ] 32 tests.
16/54 Test #16: MDSpanTests ......................... Passed 0.02 sec
test 17
Start 17: OnlineHelpUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 22 tests from 4 test cases.
17: [----------] Global test environment set-up.
17: [----------] 6 tests from TextTableFormatterTest
17: [ RUN ] TextTableFormatterTest.HandlesBasicCase
17: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesIndentation
17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
17: [----------] 6 tests from TextTableFormatterTest (2 ms total)
17:
17: [----------] 3 tests from HelpManagerTest
17: [ RUN ] HelpManagerTest.HandlesRootTopic
17: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
17: [ RUN ] HelpManagerTest.HandlesSubTopics
17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
17: [ RUN ] HelpManagerTest.HandlesInvalidTopics
17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
17: [----------] 3 tests from HelpManagerTest (1 ms total)
17:
17: [----------] 2 tests from HelpTopicFormattingTest
17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms)
17: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
17:
17: [----------] 11 tests from HelpWriterContextTest
17: [ RUN ] HelpWriterContextTest.FormatsParagraphs
17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralText
17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsBulletList
17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsGridTable
17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsTitles
17: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms)
17: [----------] 11 tests from HelpWriterContextTest (4 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 22 tests from 4 test cases ran. (8 ms total)
17: [ PASSED ] 22 tests.
17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.03 sec
test 18
Start 18: OptionsUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 110 tests from 18 test cases.
18: [----------] Global test environment set-up.
18: [----------] 5 tests from AbstractOptionStorageTest
18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
18: [----------] 5 tests from AbstractOptionStorageTest (2 ms total)
18:
18: [----------] 8 tests from FileNameOptionTest
18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
18: [----------] 8 tests from FileNameOptionTest (1 ms total)
18:
18: [----------] 15 tests from FileNameOptionManagerTest
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (1 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
18: [----------] 15 tests from FileNameOptionManagerTest (1 ms total)
18:
18: [----------] 1 test from OptionsTest
18: [ RUN ] OptionsTest.FailsOnNonsafeStorage
18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
18: [----------] 1 test from OptionsTest (1 ms total)
18:
18: [----------] 9 tests from OptionsAssignerTest
18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMissingValue
18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesExtraValue
18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesGroups
18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesSections
18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
18: [----------] 9 tests from OptionsAssignerTest (0 ms total)
18:
18: [----------] 4 tests from OptionsAssignerBooleanTest
18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
18: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
18:
18: [----------] 13 tests from OptionsAssignerIntegerTest
18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
18: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total)
18:
18: [----------] 5 tests from OptionsAssignerDoubleTest
18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
18:
18: [----------] 9 tests from OptionsAssignerStringTest
18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (1 ms)
18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
18:
18: [----------] 6 tests from OptionsAssignerEnumTest
18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
18:
18: [----------] 8 tests from RepeatingOptionSectionTest
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (1 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
18: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
18:
18: [----------] 1 test from TimeUnitManagerTest
18: [ RUN ] TimeUnitManagerTest.BasicOperations
18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
18: [----------] 1 test from TimeUnitManagerTest (0 ms total)
18:
18: [----------] 4 tests from TimeUnitBehaviorTest
18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
18:
18: [----------] 2 tests from TreeValueSupportAssignTest
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
18:
18: [----------] 1 test from TreeValueSupportAssignErrorTest
18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
18:
18: [----------] 5 tests from TreeValueSupportCheckTest
18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
18:
18: [----------] 6 tests from TreeValueSupportAdjustTest
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms)
18: [----------] 6 tests from TreeValueSupportAdjustTest (2 ms total)
18:
18: [----------] 8 tests from TreeValueSupportTest
18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsInt64Option
18: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsStringOption
18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsFloatOption
18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumOption
18: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
18: [----------] 8 tests from TreeValueSupportTest (2 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 110 tests from 18 test cases ran. (15 ms total)
18: [ PASSED ] 110 tests.
18/54 Test #18: OptionsUnitTests .................... Passed 0.04 sec
test 19
Start 19: PbcutilUnitTest
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PbcutilUnitTest.xml"
19: Test timeout computed to be: 30
19: [==========] Running 3 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 1 test from PbcTest
19: [ RUN ] PbcTest.CalcShiftsWorks
19: [ OK ] PbcTest.CalcShiftsWorks (1 ms)
19: [----------] 1 test from PbcTest (1 ms total)
19:
19: [----------] 2 tests from PbcEnumsTest
19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
19: [----------] 2 tests from PbcEnumsTest (0 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 3 tests from 2 test cases ran. (1 ms total)
19: [ PASSED ] 3 tests.
19/54 Test #19: PbcutilUnitTest ..................... Passed 0.02 sec
test 20
Start 20: RandomUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 44 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 4 tests from ExponentialDistributionTest
20: [ RUN ] ExponentialDistributionTest.Output
20: [ OK ] ExponentialDistributionTest.Output (1 ms)
20: [ RUN ] ExponentialDistributionTest.Logical
20: [ OK ] ExponentialDistributionTest.Logical (0 ms)
20: [ RUN ] ExponentialDistributionTest.Reset
20: [ OK ] ExponentialDistributionTest.Reset (0 ms)
20: [ RUN ] ExponentialDistributionTest.AltParam
20: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
20:
20: [----------] 4 tests from GammaDistributionTest
20: [ RUN ] GammaDistributionTest.Output
20: [ OK ] GammaDistributionTest.Output (0 ms)
20: [ RUN ] GammaDistributionTest.Logical
20: [ OK ] GammaDistributionTest.Logical (0 ms)
20: [ RUN ] GammaDistributionTest.Reset
20: [ OK ] GammaDistributionTest.Reset (0 ms)
20: [ RUN ] GammaDistributionTest.AltParam
20: [ OK ] GammaDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from GammaDistributionTest (0 ms total)
20:
20: [----------] 4 tests from NormalDistributionTest
20: [ RUN ] NormalDistributionTest.Output
20: [ OK ] NormalDistributionTest.Output (1 ms)
20: [ RUN ] NormalDistributionTest.Logical
20: [ OK ] NormalDistributionTest.Logical (0 ms)
20: [ RUN ] NormalDistributionTest.Reset
20: [ OK ] NormalDistributionTest.Reset (0 ms)
20: [ RUN ] NormalDistributionTest.AltParam
20: [ OK ] NormalDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from NormalDistributionTest (1 ms total)
20:
20: [----------] 1 test from SeedTest
20: [ RUN ] SeedTest.makeRandomSeed
20: [ OK ] SeedTest.makeRandomSeed (0 ms)
20: [----------] 1 test from SeedTest (0 ms total)
20:
20: [----------] 6 tests from TabulatedNormalDistributionTest
20: [ RUN ] TabulatedNormalDistributionTest.Output14
20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Output16
20: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Logical
20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Reset
20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.AltParam
20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
20: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total)
20:
20: [----------] 1 test from TabulatedNormalDistributionTableTest
20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms)
20: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total)
20:
20: [----------] 6 tests from ThreeFry2x64Test
20: [ RUN ] ThreeFry2x64Test.Logical
20: [ OK ] ThreeFry2x64Test.Logical (0 ms)
20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
20: [ RUN ] ThreeFry2x64Test.Reseed
20: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
20: [ RUN ] ThreeFry2x64Test.Discard
20: [ OK ] ThreeFry2x64Test.Discard (0 ms)
20: [ RUN ] ThreeFry2x64Test.InvalidCounter
20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
20: [----------] 6 tests from ThreeFry2x64Test (0 ms total)
20:
20: [----------] 4 tests from UniformIntDistributionTest
20: [ RUN ] UniformIntDistributionTest.Output
20: [ OK ] UniformIntDistributionTest.Output (1 ms)
20: [ RUN ] UniformIntDistributionTest.Logical
20: [ OK ] UniformIntDistributionTest.Logical (0 ms)
20: [ RUN ] UniformIntDistributionTest.Reset
20: [ OK ] UniformIntDistributionTest.Reset (0 ms)
20: [ RUN ] UniformIntDistributionTest.AltParam
20: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
20:
20: [----------] 5 tests from UniformRealDistributionTest
20: [ RUN ] UniformRealDistributionTest.GenerateCanonical
20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Output
20: [ OK ] UniformRealDistributionTest.Output (0 ms)
20: [ RUN ] UniformRealDistributionTest.Logical
20: [ OK ] UniformRealDistributionTest.Logical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Reset
20: [ OK ] UniformRealDistributionTest.Reset (0 ms)
20: [ RUN ] UniformRealDistributionTest.AltParam
20: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
20: [----------] 5 tests from UniformRealDistributionTest (0 ms total)
20:
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (2 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 44 tests from 10 test cases ran. (9 ms total)
20: [ PASSED ] 44 tests.
20/54 Test #20: RandomUnitTests ..................... Passed 0.04 sec
test 21
Start 21: RestraintTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 1 test from 1 test case.
21: [----------] Global test environment set-up.
21: [----------] 1 test from RestraintManager
21: [ RUN ] RestraintManager.restraintList
21: [ OK ] RestraintManager.restraintList (0 ms)
21: [----------] 1 test from RestraintManager (0 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 1 test from 1 test case ran. (0 ms total)
21: [ PASSED ] 1 test.
21/54 Test #21: RestraintTests ...................... Passed 0.02 sec
test 22
Start 22: TableUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 16 tests from 2 test cases.
22: [----------] Global test environment set-up.
22: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms)
22: [ RUN ] SplineTableTest/0.Sinc
22: [ OK ] SplineTableTest/0.Sinc (2 ms)
22: [ RUN ] SplineTableTest/0.LJ12
22: [ OK ] SplineTableTest/0.LJ12 (25 ms)
22: [ RUN ] SplineTableTest/0.PmeCorrection
22: [ OK ] SplineTableTest/0.PmeCorrection (3 ms)
22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms)
22: [ RUN ] SplineTableTest/0.TwoFunctions
22: [ OK ] SplineTableTest/0.TwoFunctions (51 ms)
22: [ RUN ] SplineTableTest/0.ThreeFunctions
22: [ OK ] SplineTableTest/0.ThreeFunctions (57 ms)
22: [----------] 8 tests from SplineTableTest/0 (143 ms total)
22:
22: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (3 ms)
22: [ RUN ] SplineTableTest/1.Sinc
22: [ OK ] SplineTableTest/1.Sinc (1 ms)
22: [ RUN ] SplineTableTest/1.LJ12
22: [ OK ] SplineTableTest/1.LJ12 (4 ms)
22: [ RUN ] SplineTableTest/1.PmeCorrection
22: [ OK ] SplineTableTest/1.PmeCorrection (3 ms)
22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
22: [ RUN ] SplineTableTest/1.TwoFunctions
22: [ OK ] SplineTableTest/1.TwoFunctions (7 ms)
22: [ RUN ] SplineTableTest/1.ThreeFunctions
22: [ OK ] SplineTableTest/1.ThreeFunctions (8 ms)
22: [----------] 8 tests from SplineTableTest/1 (30 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 16 tests from 2 test cases ran. (174 ms total)
22: [ PASSED ] 16 tests.
22/54 Test #22: TableUnitTests ...................... Passed 0.19 sec
test 23
Start 23: TaskAssignmentUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 3 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (1 ms total)
23:
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms)
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 3 tests from 2 test cases ran. (3 ms total)
23: [ PASSED ] 3 tests.
23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.02 sec
test 24
Start 24: TopologyTest
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TopologyTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 11 tests from 3 test cases.
24: [----------] Global test environment set-up.
24: [----------] 3 tests from ExclusionBlockTest
24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
24: [ RUN ] ExclusionBlockTest.MergeExclusions
24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
24: [----------] 3 tests from ExclusionBlockTest (0 ms total)
24:
24: [----------] 2 tests from MtopTest
24: [ RUN ] MtopTest.RangeBasedLoop
24: [ OK ] MtopTest.RangeBasedLoop (0 ms)
24: [ RUN ] MtopTest.Operators
24: [ OK ] MtopTest.Operators (0 ms)
24: [----------] 2 tests from MtopTest (0 ms total)
24:
24: [----------] 6 tests from SymtabTest
24: [ RUN ] SymtabTest.EmptyOnOpen
24: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
24: [ RUN ] SymtabTest.AddSingleEntry
24: [ OK ] SymtabTest.AddSingleEntry (0 ms)
24: [ RUN ] SymtabTest.AddTwoDistinctEntries
24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
24: [ RUN ] SymtabTest.TryToAddDuplicates
24: [ OK ] SymtabTest.TryToAddDuplicates (1 ms)
24: [ RUN ] SymtabTest.AddLargeNumberOfEntries
24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms)
24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms)
24: [----------] 6 tests from SymtabTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 11 tests from 3 test cases ran. (2 ms total)
24: [ PASSED ] 11 tests.
24/54 Test #24: TopologyTest ........................ Passed 0.02 sec
test 25
Start 25: PullTest
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 5 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 5 tests from PullTest
25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
25: [----------] 5 tests from PullTest (1 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 5 tests from 1 test case ran. (1 ms total)
25: [ PASSED ] 5 tests.
25/54 Test #25: PullTest ............................ Passed 0.02 sec
test 26
Start 26: AwhTest
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 12 tests from 4 test cases.
26: [----------] Global test environment set-up.
26: [----------] 1 test from BiasTest
26: [ RUN ] BiasTest.DetectsCovering
26: [ OK ] BiasTest.DetectsCovering (1 ms)
26: [----------] 1 test from BiasTest (1 ms total)
26:
26: [----------] 1 test from gridTest
26: [ RUN ] gridTest.neighborhood
26: [ OK ] gridTest.neighborhood (3 ms)
26: [----------] 1 test from gridTest (3 ms total)
26:
26: [----------] 8 tests from WithParameters/BiasTest
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms)
26: [----------] 8 tests from WithParameters/BiasTest (7 ms total)
26:
26: [----------] 2 tests from WithParameters/BiasStateTest
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms)
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 12 tests from 4 test cases ran. (12 ms total)
26: [ PASSED ] 12 tests.
26/54 Test #26: AwhTest ............................. Passed 0.03 sec
test 27
Start 27: SimdUnitTests
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 86 tests from 3 test cases.
27: [----------] Global test environment set-up.
27: [----------] 41 tests from SimdScalarTest
27: [ RUN ] SimdScalarTest.load
27: [ OK ] SimdScalarTest.load (0 ms)
27: [ RUN ] SimdScalarTest.loadU
27: [ OK ] SimdScalarTest.loadU (0 ms)
27: [ RUN ] SimdScalarTest.store
27: [ OK ] SimdScalarTest.store (0 ms)
27: [ RUN ] SimdScalarTest.storeU
27: [ OK ] SimdScalarTest.storeU (0 ms)
27: [ RUN ] SimdScalarTest.setZero
27: [ OK ] SimdScalarTest.setZero (0 ms)
27: [ RUN ] SimdScalarTest.andNot
27: [ OK ] SimdScalarTest.andNot (0 ms)
27: [ RUN ] SimdScalarTest.fma
27: [ OK ] SimdScalarTest.fma (0 ms)
27: [ RUN ] SimdScalarTest.fms
27: [ OK ] SimdScalarTest.fms (0 ms)
27: [ RUN ] SimdScalarTest.fnma
27: [ OK ] SimdScalarTest.fnma (0 ms)
27: [ RUN ] SimdScalarTest.fnms
27: [ OK ] SimdScalarTest.fnms (0 ms)
27: [ RUN ] SimdScalarTest.maskAdd
27: [ OK ] SimdScalarTest.maskAdd (0 ms)
27: [ RUN ] SimdScalarTest.maskzMul
27: [ OK ] SimdScalarTest.maskzMul (0 ms)
27: [ RUN ] SimdScalarTest.maskzFma
27: [ OK ] SimdScalarTest.maskzFma (0 ms)
27: [ RUN ] SimdScalarTest.abs
27: [ OK ] SimdScalarTest.abs (0 ms)
27: [ RUN ] SimdScalarTest.max
27: [ OK ] SimdScalarTest.max (0 ms)
27: [ RUN ] SimdScalarTest.min
27: [ OK ] SimdScalarTest.min (0 ms)
27: [ RUN ] SimdScalarTest.round
27: [ OK ] SimdScalarTest.round (0 ms)
27: [ RUN ] SimdScalarTest.trunc
27: [ OK ] SimdScalarTest.trunc (0 ms)
27: [ RUN ] SimdScalarTest.reduce
27: [ OK ] SimdScalarTest.reduce (0 ms)
27: [ RUN ] SimdScalarTest.testBits
27: [ OK ] SimdScalarTest.testBits (0 ms)
27: [ RUN ] SimdScalarTest.anyTrue
27: [ OK ] SimdScalarTest.anyTrue (0 ms)
27: [ RUN ] SimdScalarTest.selectByMask
27: [ OK ] SimdScalarTest.selectByMask (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMask
27: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
27: [ RUN ] SimdScalarTest.blend
27: [ OK ] SimdScalarTest.blend (0 ms)
27: [ RUN ] SimdScalarTest.cvtR2I
27: [ OK ] SimdScalarTest.cvtR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvttR2I
27: [ OK ] SimdScalarTest.cvttR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvtI2R
27: [ OK ] SimdScalarTest.cvtI2R (0 ms)
27: [ RUN ] SimdScalarTest.cvtF2D
27: [ OK ] SimdScalarTest.cvtF2D (0 ms)
27: [ RUN ] SimdScalarTest.cvtD2D
27: [ OK ] SimdScalarTest.cvtD2D (0 ms)
27: [ RUN ] SimdScalarTest.loadI
27: [ OK ] SimdScalarTest.loadI (0 ms)
27: [ RUN ] SimdScalarTest.loadUI
27: [ OK ] SimdScalarTest.loadUI (0 ms)
27: [ RUN ] SimdScalarTest.storeI
27: [ OK ] SimdScalarTest.storeI (0 ms)
27: [ RUN ] SimdScalarTest.storeUI
27: [ OK ] SimdScalarTest.storeUI (0 ms)
27: [ RUN ] SimdScalarTest.andNotI
27: [ OK ] SimdScalarTest.andNotI (0 ms)
27: [ RUN ] SimdScalarTest.testBitsI
27: [ OK ] SimdScalarTest.testBitsI (0 ms)
27: [ RUN ] SimdScalarTest.selectByMaskI
27: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMaskI
27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
27: [ RUN ] SimdScalarTest.blendI
27: [ OK ] SimdScalarTest.blendI (0 ms)
27: [ RUN ] SimdScalarTest.cvtB2IB
27: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
27: [ RUN ] SimdScalarTest.cvtIB2B
27: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
27: [ RUN ] SimdScalarTest.expandScalarsToTriplets
27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
27: [----------] 41 tests from SimdScalarTest (1 ms total)
27:
27: [----------] 8 tests from SimdScalarUtilTest
27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (1 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
27: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
27:
27: [----------] 37 tests from SimdScalarMathTest
27: [ RUN ] SimdScalarMathTest.copysign
27: [ OK ] SimdScalarMathTest.copysign (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPair
27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
27: [ RUN ] SimdScalarMathTest.inv
27: [ OK ] SimdScalarMathTest.inv (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrt
27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
27: [ RUN ] SimdScalarMathTest.log
27: [ OK ] SimdScalarMathTest.log (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2
27: [ OK ] SimdScalarMathTest.exp2 (0 ms)
27: [ RUN ] SimdScalarMathTest.exp
27: [ OK ] SimdScalarMathTest.exp (0 ms)
27: [ RUN ] SimdScalarMathTest.erf
27: [ OK ] SimdScalarMathTest.erf (0 ms)
27: [ RUN ] SimdScalarMathTest.erfc
27: [ OK ] SimdScalarMathTest.erfc (0 ms)
27: [ RUN ] SimdScalarMathTest.sincos
27: [ OK ] SimdScalarMathTest.sincos (0 ms)
27: [ RUN ] SimdScalarMathTest.sin
27: [ OK ] SimdScalarMathTest.sin (0 ms)
27: [ RUN ] SimdScalarMathTest.cos
27: [ OK ] SimdScalarMathTest.cos (0 ms)
27: [ RUN ] SimdScalarMathTest.tan
27: [ OK ] SimdScalarMathTest.tan (0 ms)
27: [ RUN ] SimdScalarMathTest.asin
27: [ OK ] SimdScalarMathTest.asin (0 ms)
27: [ RUN ] SimdScalarMathTest.acos
27: [ OK ] SimdScalarMathTest.acos (0 ms)
27: [ RUN ] SimdScalarMathTest.atan
27: [ OK ] SimdScalarMathTest.atan (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2
27: [ OK ] SimdScalarMathTest.atan2 (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrection
27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.invSingleAccuracy
27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.logSingleAccuracy
27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.expSingleAccuracy
27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
27: [----------] 37 tests from SimdScalarMathTest (1 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 86 tests from 3 test cases ran. (3 ms total)
27: [ PASSED ] 86 tests.
27/54 Test #27: SimdUnitTests ....................... Passed 0.03 sec
test 28
Start 28: CompatibilityHelpersTests
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 170 tests from 12 test cases.
28: [----------] Global test environment set-up.
28: [----------] 45 tests from OptionalTest
28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructEmpty
28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
28: [ RUN ] OptionalTest.CanConstructFromNullopt
28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValue
28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValue
28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromValue
28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignFromValue
28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanResetContent
28: [ OK ] OptionalTest.CanResetContent (0 ms)
28: [ RUN ] OptionalTest.ProvidesRelationalOperators
28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms)
28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (1 ms)
28: [ RUN ] OptionalTest.CanProduceHash
28: [ OK ] OptionalTest.CanProduceHash (0 ms)
28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
28: alignment_of<char>: 1
28: alignment_of<short>: 2
28: alignment_of<int>: 4
28: alignment_of<long>: 4
28: alignment_of<float>: 4
28: alignment_of<double>: 8
28: alignment_of<long double>: 8
28: alignment_of<Struct>: 1
28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
28: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
28: sizeof( optional<char> ): 2 (1)
28: sizeof( optional<short> ): 4 (2)
28: sizeof( optional<int> ): 8 (4)
28: sizeof( optional<long> ): 8 (4)
28: sizeof( optional<float> ): 8 (4)
28: sizeof( optional<double> ): 16 (8)
28: sizeof( optional<long double> ): 16 (8)
28: sizeof( optional<Struct> ): 2 (1)
28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
28: [----------] 45 tests from OptionalTest (4 ms total)
28:
28: [----------] 7 tests from MakeOptionalTest
28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] MakeOptionalTest.CanCopyConstruct
28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanMoveConstruct
28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (1 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
28: [----------] 7 tests from MakeOptionalTest (1 ms total)
28:
28: [----------] 4 tests from OptionalMemberSwapTest
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
28:
28: [----------] 4 tests from OptionalImplicitValueTest
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total)
28:
28: [----------] 20 tests from OptionalIntValueTest
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (1 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
28: [----------] 20 tests from OptionalIntValueTest (2 ms total)
28:
28: [----------] 1 test from NotNullConstruction
28: [ RUN ] NotNullConstruction.Works
28: [ OK ] NotNullConstruction.Works (0 ms)
28: [----------] 1 test from NotNullConstruction (0 ms total)
28:
28: [----------] 1 test from NotNullCasting
28: [ RUN ] NotNullCasting.Works
28: [ OK ] NotNullCasting.Works (0 ms)
28: [----------] 1 test from NotNullCasting (0 ms total)
28:
28: [----------] 1 test from NotNullAssignment
28: [ RUN ] NotNullAssignment.Works
28: [ OK ] NotNullAssignment.Works (0 ms)
28: [----------] 1 test from NotNullAssignment (0 ms total)
28:
28: [----------] 1 test from MakeNotNull
28: [ RUN ] MakeNotNull.Works
28: [ OK ] MakeNotNull.Works (0 ms)
28: [----------] 1 test from MakeNotNull (0 ms total)
28:
28: [----------] 1 test from NotNull
28: [ RUN ] NotNull.WorksInContainers
28: [ OK ] NotNull.WorksInContainers (0 ms)
28: [----------] 1 test from NotNull (0 ms total)
28:
28: [----------] 80 tests from StringViewTest
28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromCString
28: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (1 ms)
28: [ RUN ] StringViewTest.AllowForwardIteration
28: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstForwardIteration
28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowReverseIteration
28: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstReverseIteration
28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaAt
28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
28: [ RUN ] StringViewTest.CanAccessAllElementsViaData
28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
28: [ RUN ] StringViewTest.CanRemovePrefix
28: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
28: [ RUN ] StringViewTest.CanRemoveSuffix
28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
28: [ RUN ] StringViewTest.CanSwapWithOtherView
28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
28: [ RUN ] StringViewTest.CanCopySubstringWithCopy
28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (1 ms)
28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (1 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCompareToViews
28: [ OK ] StringViewTest.CanCompareToViews (0 ms)
28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (1 ms)
28: [ RUN ] StringViewTest.CanPrintViewToPutputStream
28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
28: [----------] 80 tests from StringViewTest (5 ms total)
28:
28: [----------] 5 tests from StringViewExtensionTest
28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
28: [----------] 5 tests from StringViewExtensionTest (0 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 170 tests from 12 test cases ran. (12 ms total)
28: [ PASSED ] 170 tests.
28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.04 sec
test 29
Start 29: GmxAnaTest
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
29: Test timeout computed to be: 600
29: [==========] Running 27 tests from 5 test cases.
29: [----------] Global test environment set-up.
29: [----------] 5 tests from Entropy
29: [ RUN ] Entropy.Schlitter_300_NoLinear
29: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms)
29: [ RUN ] Entropy.Schlitter_300_Linear
29: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_Linear
29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
29: [----------] 5 tests from Entropy (1 ms total)
29:
29: [----------] 10 tests from MindistTest
29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (3 ms)
29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms)
29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (2 ms)
29: [ RUN ] MindistTest.mindistPicksUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistPicksUpContacts (2 ms)
29: [ RUN ] MindistTest.ngWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.ngWorks (3 ms)
29: [ RUN ] MindistTest.groupWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.groupWorks (2 ms)
29: [ RUN ] MindistTest.maxDistWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.maxDistWorks (2 ms)
29: [ RUN ] MindistTest.noPbcWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.noPbcWorks (3 ms)
29: [ RUN ] MindistTest.resPerTimeWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.resPerTimeWorks (2 ms)
29: [ RUN ] MindistTest.matrixWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 5: 'atoms123'
29: Special case: making distance matrix between all atoms in group atoms123
29: [ OK ] MindistTest.matrixWorks (2 ms)
29: [----------] 10 tests from MindistTest (25 ms total)
29:
29: [----------] 3 tests from MsdTest
29: [ RUN ] MsdTest.threeDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.threeDimensionalDiffusion (3 ms)
29: [ RUN ] MsdTest.twoDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.twoDimensionalDiffusion (3 ms)
29: [ RUN ] MsdTest.oneDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.oneDimensionalDiffusion (2 ms)
29: [----------] 3 tests from MsdTest (8 ms total)
29:
29: [----------] 3 tests from MsdMolTest
29: [ RUN ] MsdMolTest.diffMolMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -23119927
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolMassWeighted (858 ms)
29: [ RUN ] MsdMolTest.diffMolNonMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -279183377
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolNonMassWeighted (849 ms)
29: [ RUN ] MsdMolTest.diffMolSelected
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -1677993993
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( mol) has 9 elements
29: There is one group in the index
29: Split group of 9 atoms into 3 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolSelected (849 ms)
29: [----------] 3 tests from MsdMolTest (2557 ms total)
29:
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: trr version: GMX_trn_file (single precision)
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (3 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (6 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (3 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from gro file '', 6 atoms.
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (4 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
29:
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (3 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms)
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (23 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 27 tests from 5 test cases ran. (2614 ms total)
29: [ PASSED ] 27 tests.
29/54 Test #29: GmxAnaTest .......................... Passed 2.64 sec
test 30
Start 30: GmxPreprocessTests
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 69 tests from 10 test cases.
30: [----------] Global test environment set-up.
30: [----------] 4 tests from GenconfTest
30: [ RUN ] GenconfTest.nbox_Works
30: [ OK ] GenconfTest.nbox_Works (2 ms)
30: [ RUN ] GenconfTest.nbox_norenumber_Works
30: [ OK ] GenconfTest.nbox_norenumber_Works (2 ms)
30: [ RUN ] GenconfTest.nbox_dist_Works
30: [ OK ] GenconfTest.nbox_dist_Works (2 ms)
30: [ RUN ] GenconfTest.nbox_rot_Works
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: [ OK ] GenconfTest.nbox_rot_Works (2 ms)
30: [----------] 4 tests from GenconfTest (8 ms total)
30:
30: [----------] 2 tests from GenionTest
30: [ RUN ] GenionTest.HighConcentrationIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 720633753
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
30: Group 0 ( System) has 653 elements
30: Group 1 ( Water) has 648 elements
30: Group 2 ( SOL) has 648 elements
30: Group 3 ( non-Water) has 5 elements
30: Group 4 ( Other) has 5 elements
30: Group 5 ( METH) has 5 elements
30: Select a group: Number of (3-atomic) solvent molecules: 216
30: Using random seed 1997.
30: Replacing solvent molecule 56 (atom 168) with NA
30: Replacing solvent molecule 120 (atom 360) with NA
30: Replacing solvent molecule 182 (atom 546) with NA
30: Replacing solvent molecule 71 (atom 213) with NA
30: Replacing solvent molecule 189 (atom 567) with CL
30: Replacing solvent molecule 54 (atom 162) with CL
30: Replacing solvent molecule 155 (atom 465) with CL
30: Replacing solvent molecule 99 (atom 297) with CL
30:
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: Will try to add 4 NA ions and 4 CL ions.
30: Select a continuous group of solvent molecules
30: Selected 1: 'Water'
30: [ OK ] GenionTest.HighConcentrationIonPlacement (876 ms)
30: [ RUN ] GenionTest.NoIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -2098337
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
30: No ions to add, will just copy input configuration.
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: [ OK ] GenionTest.NoIonPlacement (866 ms)
30: [----------] 2 tests from GenionTest (1742 ms total)
30:
30: [----------] 1 test from GenRestrTest
30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
30:
30: Reading structure file
30: Group 0 ( System) has 156 elements
30: Group 1 ( Protein) has 156 elements
30: Group 2 ( Protein-H) has 75 elements
30: Group 3 ( C-alpha) has 10 elements
30: Group 4 ( Backbone) has 30 elements
30: Group 5 ( MainChain) has 40 elements
30: Group 6 ( MainChain+Cb) has 49 elements
30: Group 7 ( MainChain+H) has 52 elements
30: Group 8 ( SideChain) has 104 elements
30: Group 9 ( SideChain-H) has 35 elements
30: Select a group: Select group to position restrain
30: Selected 3: 'C-alpha'
30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (6 ms)
30: [----------] 1 test from GenRestrTest (6 ms total)
30:
30: [----------] 9 tests from PreprocessingAtomTypesTest
30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total)
30:
30: [----------] 10 tests from PreprocessingBondAtomTypeTest
30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (1 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total)
30:
30: [----------] 5 tests from InsertMoleculesTest
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
30: Added 1 molecules (out of 1 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
30:
30: Output configuration contains 8 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3 success (now 6 atoms)!
30:
Try 4 success (now 8 atoms)!
30:
Try 5 success (now 10 atoms)!
30:
30: Added 5 molecules (out of 5 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
30:
30: Output configuration contains 10 atoms in 10 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
Try 2 success (now 10 atoms)!
30:
30: Added 2 molecules (out of 2 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
30:
30: Output configuration contains 10 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 650 atoms)!
30:
Try 2 success (now 652 atoms)!
30:
Try 3 success (now 654 atoms)!
30:
Try 4 success (now 656 atoms)!
30:
30: Added 4 molecules (out of 4 requested)
30: Replaced 8 residues (24 atoms)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
30:
30: Output configuration contains 632 atoms in 212 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (19 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
30:
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
30:
Try 13 success (now 6 atoms)!
30:
30: Added 3 molecules (out of 4 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
30:
30: Output configuration contains 6 atoms in 3 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (5 ms)
30: [----------] 5 tests from InsertMoleculesTest (36 ms total)
30:
30: [----------] 14 tests from GetIrTest
30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
30: Ignoring obsolete mdp entry 'title'
30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (7 ms)
30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (10 ms)
30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (7 ms)
30: [ RUN ] GetIrTest.RejectsValueWithoutKey
30: [ OK ] GetIrTest.RejectsValueWithoutKey (9 ms)
30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (9 ms)
30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (7 ms)
30: [ RUN ] GetIrTest.AcceptsEmptyLines
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsEmptyLines (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricField
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricField (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (7 ms)
30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (4 ms)
30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (7 ms)
30: [ RUN ] GetIrTest.RejectsImplicitSolventYes
30: [ OK ] GetIrTest.RejectsImplicitSolventYes (9 ms)
30: [ RUN ] GetIrTest.AcceptsMimic
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsMimic (9 ms)
30: [----------] 14 tests from GetIrTest (106 ms total)
30:
30: [----------] 5 tests from SolvateTest
30: [ RUN ] SolvateTest.cs_box_Works
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 1x1x1 boxes
30: Solvent box contains 270 atoms in 90 residues
30: Removed 129 solvent atoms due to solvent-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 47 residues
30: Generated solvent containing 141 atoms in 47 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
30:
30: Output configuration contains 141 atoms in 47 residues
30: Volume : 1.331 (nm^3)
30: Density : 1056.36 (g/l)
30: Number of solvent molecules: 47
30:
30: [ OK ] SolvateTest.cs_box_Works (20 ms)
30: [ RUN ] SolvateTest.cs_cp_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: [ OK ] SolvateTest.cs_cp_Works (99 ms)
30: [ RUN ] SolvateTest.cs_cp_p_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: Processing topology
30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
30: [ OK ] SolvateTest.cs_cp_p_Works (100 ms)
30: [ RUN ] SolvateTest.shell_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 1902 solvent atoms more than 1.000000 nm from solute.
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 252 residues
30: Generated solvent containing 756 atoms in 252 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
30:
30: Output configuration contains 762 atoms in 254 residues
30: Volume : 27.2709 (nm^3)
30: Density : 279.3 (g/l)
30: Number of solvent molecules: 252
30:
30: [ OK ] SolvateTest.shell_Works (48 ms)
30: [ RUN ] SolvateTest.update_Topology_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 3x3x3 boxes
30: Solvent box contains 14952 atoms in 4984 residues
30: Removed 2787 solvent atoms due to solvent-solvent overlap
30: Removed 30 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 2 different molecule types:
30: HOH ( 3 atoms): 1876 residues
30: SOL ( 3 atoms): 2169 residues
30: Generated solvent containing 0 atoms in 0 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
30:
30: Output configuration contains 12141 atoms in 4047 residues
30: Volume : 125 (nm^3)
30: Density : 968.963 (g/l)
30: Number of solvent molecules: 4045
30:
30: Processing topology
30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: [ OK ] SolvateTest.update_Topology_Works (399 ms)
30: [----------] 5 tests from SolvateTest (666 ms total)
30:
30: [----------] 1 test from TopDirTests
30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
30: [----------] 1 test from TopDirTests (0 ms total)
30:
30: [----------] 18 tests from SinglePeptideFragments/EditconfTest
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (15 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (14 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (13 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (8 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (6 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (6 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (10 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (7 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (7 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (13 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (12 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (11 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (6 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (4 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (5 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (7 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (6 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (6 ms)
30: [----------] 18 tests from SinglePeptideFragments/EditconfTest (157 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 69 tests from 10 test cases ran. (2722 ms total)
30: [ PASSED ] 69 tests.
30/54 Test #30: GmxPreprocessTests .................. Passed 2.75 sec
test 31
Start 31: Pdb2gmx1Test
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx1Test.xml"
31: Test timeout computed to be: 30
31: [==========] Running 24 tests from 1 test case.
31: [----------] Global test environment set-up.
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (178 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (196 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (181 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (164 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (191 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (210 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (197 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (179 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (177 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (198 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (181 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (165 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (191 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (211 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (197 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (178 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (177 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (197 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (181 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (165 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (191 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (208 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (198 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (179 ms)
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (4492 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 24 tests from 1 test case ran. (4492 ms total)
31: [ PASSED ] 24 tests.
31/54 Test #31: Pdb2gmx1Test ........................ Passed 4.51 sec
test 32
Start 32: Pdb2gmx2Test
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx2Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 32 tests from 2 test cases.
32: [----------] Global test environment set-up.
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (129 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (143 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (128 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (120 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (130 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (148 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (132 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (123 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (124 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (141 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (127 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (118 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (129 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (147 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (132 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (123 ms)
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (2096 ms total)
32:
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (136 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (154 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (139 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (131 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (141 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (161 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (143 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (135 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (136 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (155 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (138 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (130 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (141 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (161 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (143 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (135 ms)
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (2280 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 32 tests from 2 test cases ran. (4376 ms total)
32: [ PASSED ] 32 tests.
32/54 Test #32: Pdb2gmx2Test ........................ Passed 4.40 sec
test 33
Start 33: Pdb2gmx3Test
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx3Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 28 tests from 4 test cases.
33: [----------] Global test environment set-up.
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (172 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (190 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (173 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (155 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (183 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (201 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (190 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (167 ms)
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (1431 ms total)
33:
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (163 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (181 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (165 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (149 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (174 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (193 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (180 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (161 ms)
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (1368 ms total)
33:
33: [----------] 8 tests from ChainSep/Pdb2gmxTest
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (164 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 7 acceptors were found.
33: There are 7 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS8
33: NE223
33: MET12 SD55 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 125, now 125
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 317 pairs
33: Before cleaning: 322 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 5 cmap torsion pairs
33: There are 322 dihedrals, 19 impropers, 227 angles
33: 314 pairs, 125 bonds and 0 virtual sites
33: Total mass 846.083 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 7 58
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (58 atoms, 7 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 7 residues with 124 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 124 atoms 7 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (122 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (164 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 12 acceptors were found.
33: There are 13 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3
33: SG9
33: HIS8 NE251 1.055
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 115, now 115
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 288 pairs
33: Before cleaning: 293 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 6 cmap torsion pairs
33: There are 293 dihedrals, 23 impropers, 203 angles
33: 285 pairs, 115 bonds and 0 virtual sites
33: Total mass 888.952 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 8 61
33: 2 'B' 3 25
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (61 atoms, 8 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 8 residues with 114 atoms
33: Chain time...
33: Processing chain 2 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 114 atoms 8 residues
33: Including chain 2 in system: 61 atoms 3 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (121 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 260, now 260
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 650 pairs
33: Before cleaning: 660 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 8 cmap torsion pairs
33: There are 660 dihedrals, 45 impropers, 466 angles
33: 647 pairs, 260 bonds and 0 virtual sites
33: Total mass 1900.162 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33:
33: Merged chains into joint molecule definitions at 3 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 261 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (166 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 6 donors and 4 acceptors were found.
33: There are 3 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 67, now 67
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 164 pairs
33: Before cleaning: 169 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 169 dihedrals, 13 impropers, 118 angles
33: 161 pairs, 67 bonds and 0 virtual sites
33: Total mass 472.547 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 261 atoms and 16 residues
33: Total mass in system 1900.162 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
33: They will be treated as separate chains unless you reorder your file.
33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 4 33
33: 3 'B' 3 25
33: 4 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (33 atoms, 4 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 66 atoms
33: Chain time...
33: Processing chain 3 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 4 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 66 atoms 4 residues
33: Including chain 3 in system: 61 atoms 3 residues
33: Including chain 4 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (122 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 256, now 256
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 652 pairs
33: Before cleaning: 662 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 12 cmap torsion pairs
33: There are 662 dihedrals, 47 impropers, 460 angles
33: 649 pairs, 256 bonds and 0 virtual sites
33: Total mass 1864.131 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33:
33: Merged chains into joint molecule definitions at 1 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (162 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 14 donors and 15 acceptors were found.
33: There are 20 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 173, now 173
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 441 pairs
33: Before cleaning: 446 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 9 cmap torsion pairs
33: There are 446 dihedrals, 29 impropers, 312 angles
33: 438 pairs, 173 bonds and 0 virtual sites
33: Total mass 1262.488 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 255 atoms and 16 residues
33: Total mass in system 1864.131 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 11 86
33: 2 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (86 atoms, 11 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 11 residues with 172 atoms
33: Chain time...
33: Processing chain 2 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 172 atoms 11 residues
33: Including chain 2 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (126 ms)
33: [----------] 8 tests from ChainSep/Pdb2gmxTest (1147 ms total)
33:
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (82 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (81 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (81 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (82 ms)
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (327 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 28 tests from 4 test cases ran. (4273 ms total)
33: [ PASSED ] 28 tests.
33/54 Test #33: Pdb2gmx3Test ........................ Passed 4.30 sec
test 34
Start 34: CorrelationsTest
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
34: Test timeout computed to be: 30
34: [==========] Running 21 tests from 3 test cases.
34: [----------] Global test environment set-up.
34: [----------] 10 tests from AutocorrTest
34: [ RUN ] AutocorrTest.EacNormal
34: [ OK ] AutocorrTest.EacNormal (21 ms)
34: [ RUN ] AutocorrTest.EacNoNormalize
34: [ OK ] AutocorrTest.EacNoNormalize (16 ms)
34: [ RUN ] AutocorrTest.EacCos
34: [ OK ] AutocorrTest.EacCos (29 ms)
34: [ RUN ] AutocorrTest.EacVector
34: [ OK ] AutocorrTest.EacVector (43 ms)
34: [ RUN ] AutocorrTest.EacRcross
34: [ OK ] AutocorrTest.EacRcross (3 ms)
34: [ RUN ] AutocorrTest.EacP0
34: [ OK ] AutocorrTest.EacP0 (42 ms)
34: [ RUN ] AutocorrTest.EacP1
34: [ OK ] AutocorrTest.EacP1 (43 ms)
34: [ RUN ] AutocorrTest.EacP2
34: [ OK ] AutocorrTest.EacP2 (83 ms)
34: [ RUN ] AutocorrTest.EacP3
34: [ OK ] AutocorrTest.EacP3 (10 ms)
34: [ RUN ] AutocorrTest.EacP4
34: [ OK ] AutocorrTest.EacP4 (43 ms)
34: [----------] 10 tests from AutocorrTest (342 ms total)
34:
34: [----------] 1 test from ManyAutocorrelationTest
34: [ RUN ] ManyAutocorrelationTest.Empty
34: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
34: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
34:
34: [----------] 10 tests from ExpfitTest
34: [ RUN ] ExpfitTest.EffnEXP1
34: [ OK ] ExpfitTest.EffnEXP1 (2 ms)
34: [ RUN ] ExpfitTest.EffnEXP2
34: [ OK ] ExpfitTest.EffnEXP2 (3 ms)
34: [ RUN ] ExpfitTest.EffnEXPEXP
34: [ OK ] ExpfitTest.EffnEXPEXP (4 ms)
34: [ RUN ] ExpfitTest.EffnEXP5
34: [ OK ] ExpfitTest.EffnEXP5 (14 ms)
34: [ RUN ] ExpfitTest.EffnEXP7
34: [ OK ] ExpfitTest.EffnEXP7 (9 ms)
34: [ RUN ] ExpfitTest.EffnEXP9
34: [ OK ] ExpfitTest.EffnEXP9 (69 ms)
34: [ RUN ] ExpfitTest.EffnERF
34: [ OK ] ExpfitTest.EffnERF (8 ms)
34: [ RUN ] ExpfitTest.EffnERREST
34: [ OK ] ExpfitTest.EffnERREST (2 ms)
34: [ RUN ] ExpfitTest.EffnVAC
34: [ OK ] ExpfitTest.EffnVAC (14 ms)
34: [ RUN ] ExpfitTest.EffnPRES
34: [ OK ] ExpfitTest.EffnPRES (38 ms)
34: [----------] 10 tests from ExpfitTest (165 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 21 tests from 3 test cases ran. (541 ms total)
34: [ PASSED ] 21 tests.
34/54 Test #34: CorrelationsTest .................... Passed 0.56 sec
test 35
Start 35: AnalysisDataUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 69 tests from 14 test cases.
35: [----------] Global test environment set-up.
35: [----------] 3 tests from AnalysisDataInitializationTest
35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
35: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/0 (25 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/1 (29 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (6 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (8 ms)
35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (3 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (3 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/2 (36 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (8 ms)
35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (3 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/3 (35 ms total)
35:
35: [----------] 4 tests from AnalysisArrayDataTest
35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisArrayDataTest.StorageWorks
35: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
35: [----------] 4 tests from AnalysisArrayDataTest (6 ms total)
35:
35: [----------] 6 tests from AverageModuleTest
35: [ RUN ] AverageModuleTest.BasicTest
35: [ OK ] AverageModuleTest.BasicTest (4 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipointData
35: [ OK ] AverageModuleTest.HandlesMultipointData (4 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeXAxis
35: [ OK ] AverageModuleTest.CanCustomizeXAxis (5 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
35: [----------] 6 tests from AverageModuleTest (28 ms total)
35:
35: [----------] 2 tests from FrameAverageModuleTest
35: [ RUN ] FrameAverageModuleTest.BasicTest
35: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 2 tests from FrameAverageModuleTest (9 ms total)
35:
35: [----------] 7 tests from AnalysisHistogramSettingsTest
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
35: [----------] 7 tests from AnalysisHistogramSettingsTest (1 ms total)
35:
35: [----------] 2 tests from SimpleHistogramModuleTest
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [----------] 2 tests from SimpleHistogramModuleTest (12 ms total)
35:
35: [----------] 3 tests from WeightedHistogramModuleTest
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (7 ms)
35: [----------] 3 tests from WeightedHistogramModuleTest (19 ms total)
35:
35: [----------] 3 tests from BinAverageModuleTest
35: [ RUN ] BinAverageModuleTest.ComputesCorrectly
35: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (5 ms)
35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 3 tests from BinAverageModuleTest (16 ms total)
35:
35: [----------] 4 tests from AbstractAverageHistogramTest
35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (11 ms)
35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (6 ms)
35: [----------] 4 tests from AbstractAverageHistogramTest (30 ms total)
35:
35: [----------] 3 tests from LifetimeModuleTest
35: [ RUN ] LifetimeModuleTest.BasicTest
35: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
35: [ RUN ] LifetimeModuleTest.CumulativeTest
35: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (4 ms)
35: [----------] 3 tests from LifetimeModuleTest (12 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 69 tests from 14 test cases ran. (261 ms total)
35: [ PASSED ] 69 tests.
35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.29 sec
test 36
Start 36: CoordinateIOTests
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CoordinateIOTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 64 tests from 19 test cases.
36: [----------] Global test environment set-up.
36: [----------] 1 test from OutputSelectorDeathTest
36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (12 ms)
36: [----------] 1 test from OutputSelectorDeathTest (12 ms total)
36:
36: [----------] 5 tests from TrajectoryFrameWriterTest
36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (17 ms)
36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
36: [----------] 5 tests from TrajectoryFrameWriterTest (44 ms total)
36:
36: [----------] 5 tests from OutputAdapterContainer
36: [ RUN ] OutputAdapterContainer.MakeEmpty
36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
36: [ RUN ] OutputAdapterContainer.AddAdapter
36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectBadAdapter
36: [ OK ] OutputAdapterContainer.RejectBadAdapter (1 ms)
36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
36: [----------] 5 tests from OutputAdapterContainer (1 ms total)
36:
36: [----------] 5 tests from FlagTest
36: [ RUN ] FlagTest.CanSetSimpleFlag
36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
36: [ RUN ] FlagTest.CanAddNewBox
36: [ OK ] FlagTest.CanAddNewBox (0 ms)
36: [ RUN ] FlagTest.SetsImplicitPrecisionChange
36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitStartTimeChange
36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitTimeStepChange
36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
36: [----------] 5 tests from FlagTest (0 ms total)
36:
36: [----------] 5 tests from SetAtomsTest
36: [ RUN ] SetAtomsTest.RemovesExistingAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.RemovesExistingAtoms (9 ms)
36: [ RUN ] SetAtomsTest.AddsNewAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.AddsNewAtoms (9 ms)
36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (9 ms)
36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (8 ms)
36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (8 ms)
36: [----------] 5 tests from SetAtomsTest (44 ms total)
36:
36: [----------] 2 tests from SetBothTimeTest
36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
36: [----------] 2 tests from SetBothTimeTest (0 ms total)
36:
36: [----------] 2 tests from SetStartTimeTest
36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
36: [ RUN ] SetStartTimeTest.WorksWithZeroStart
36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
36: [----------] 2 tests from SetStartTimeTest (0 ms total)
36:
36: [----------] 1 test from SetTimeStepTest
36: [ RUN ] SetTimeStepTest.SetTimeStepWorks
36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
36: [----------] 1 test from SetTimeStepTest (0 ms total)
36:
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (8 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (8 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (8 ms)
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (52 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (9 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (8 ms)
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (26 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total)
36:
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (18 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (18 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (19 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (18 ms)
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (73 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (9 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (8 ms)
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (26 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (8 ms)
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (8 ms)
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (17 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (1 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (8 ms)
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (17 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
36:
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (8 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (9 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (9 ms)
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (35 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 64 tests from 19 test cases ran. (352 ms total)
36: [ PASSED ] 64 tests.
36/54 Test #36: CoordinateIOTests ................... Passed 0.38 sec
test 37
Start 37: TrajectoryAnalysisUnitTests
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 82 tests from 16 test cases.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from ClustsizeTest
37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 2, cmax: 4, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (5 ms)
37: [ RUN ] ClustsizeTest.NoMolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 1, cmax: 6, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (5 ms)
37: [ RUN ] ClustsizeTest.MolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (13 ms)
37: [ RUN ] ClustsizeTest.MolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 1, cmax: 6, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms)
37: [ RUN ] ClustsizeTest.MolCSize
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolCSize (13 ms)
37: [----------] 5 tests from ClustsizeTest (48 ms total)
37:
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (8 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (18 ms total)
37:
37: [----------] 11 tests from AngleModuleTest
37: [ RUN ] AngleModuleTest.ComputesSimpleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesSimpleAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesDihedrals
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesDihedrals (10 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
37: Reading frames from gro file 'Test system for different angles', 33 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesMultipleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesMultipleAngles (16 ms)
37: [ RUN ] AngleModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (12 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (14 ms)
37: [----------] 11 tests from AngleModuleTest (132 ms total)
37:
37: [----------] 4 tests from ConvertTrjModuleTest
37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (107 ms)
37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (107 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (11 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (12 ms)
37: [----------] 4 tests from ConvertTrjModuleTest (237 ms total)
37:
37: [----------] 3 tests from DistanceModuleTest
37: [ RUN ] DistanceModuleTest.ComputesDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: [ OK ] DistanceModuleTest.ComputesDistances (14 ms)
37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
37: Number of samples: 4
37: Average distance: 1.81066 nm
37: Standard deviation: 0.79289 nm
37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (18 ms)
37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2 and res_cog x < 2.8:
37: Number of samples: 3
37: Average distance: 1.72076 nm
37: Standard deviation: 1.24839 nm
37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (15 ms)
37: [----------] 3 tests from DistanceModuleTest (47 ms total)
37:
37: [----------] 2 tests from ExtractClusterModuleTest
37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
37: trr version: GMX_trn_file (single precision)
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (12 ms)
37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (13 ms)
37: [----------] 2 tests from ExtractClusterModuleTest (25 ms total)
37:
37: [----------] 2 tests from FreeVolumeModuleTest
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for 40 particles. These were set to zero.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 13
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.02 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
37: Fractional free volume 0.194 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (770 ms)
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 17
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.48 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
37: Fractional free volume 0.200 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (768 ms)
37: [----------] 2 tests from FreeVolumeModuleTest (1538 ms total)
37:
37: [----------] 9 tests from PairDistanceModuleTest
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (10 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (10 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (8 ms)
37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (9 ms)
37: [----------] 9 tests from PairDistanceModuleTest (83 ms total)
37:
37: [----------] 5 tests from RdfModuleTest
37: [ RUN ] RdfModuleTest.BasicTest
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.BasicTest (62 ms)
37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (43 ms)
37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (61 ms)
37: [ RUN ] RdfModuleTest.CalculatesSurf
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesSurf (44 ms)
37: [ RUN ] RdfModuleTest.CalculatesXY
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesXY (71 ms)
37: [----------] 5 tests from RdfModuleTest (282 ms total)
37:
37: [----------] 5 tests from SasaModuleTest
37: [ RUN ] SasaModuleTest.BasicTest
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.BasicTest (34 ms)
37: [ RUN ] SasaModuleTest.HandlesSelectedResidues
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesSelectedResidues (22 ms)
37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (18 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (27 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (27 ms)
37: [----------] 5 tests from SasaModuleTest (131 ms total)
37:
37: [----------] 8 tests from SelectModuleTest
37: [ RUN ] SelectModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.BasicTest (18 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (13 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (13 ms)
37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (14 ms)
37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (14 ms)
37: [ RUN ] SelectModuleTest.NormalizesSizes
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.NormalizesSizes (12 ms)
37: [ RUN ] SelectModuleTest.WritesResidueNumbers
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueNumbers (8 ms)
37: [ RUN ] SelectModuleTest.WritesResidueIndices
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueIndices (8 ms)
37: [----------] 8 tests from SelectModuleTest (101 ms total)
37:
37: [----------] 10 tests from SurfaceAreaTest
37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints12
37: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints32
37: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints42
37: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints122
37: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms)
37: [ RUN ] SurfaceAreaTest.Computes100Points
37: [ OK ] SurfaceAreaTest.Computes100Points (2 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (8 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (10 ms)
37: [----------] 10 tests from SurfaceAreaTest (30 ms total)
37:
37: [----------] 4 tests from TopologyInformation
37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
37: [ RUN ] TopologyInformation.WorksWithGroFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithGroFile (8 ms)
37: [ RUN ] TopologyInformation.WorksWithPdbFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithPdbFile (8 ms)
37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -553714818
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
37:
37: NOTE 2 [file lysozyme.top, line 1465]:
37: System has non-zero total charge: 2.000000
37: Total charge should normally be an integer. See
37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
37: for discussion on how close it should be to an integer.
37:
37:
37:
37: Number of degrees of freedom in T-Coupling group rest is 465.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
37: Analysing residue names:
37: There are: 10 Protein residues
37: Analysing Protein...
37: This run will generate roughly 0 Mb of data
37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (973 ms)
37: [----------] 4 tests from TopologyInformation (990 ms total)
37:
37: [----------] 4 tests from TrajectoryModuleTest
37: [ RUN ] TrajectoryModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.BasicTest (10 ms)
37: [ RUN ] TrajectoryModuleTest.PlotsXOnly
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.PlotsXOnly (10 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (10 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoForces
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoForces (10 ms)
37: [----------] 4 tests from TrajectoryModuleTest (41 ms total)
37:
37: [----------] 5 tests from UnionFinderTest
37: [ RUN ] UnionFinderTest.WorksEmpty
37: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
37: [ RUN ] UnionFinderTest.BasicMerges
37: [ OK ] UnionFinderTest.BasicMerges (0 ms)
37: [ RUN ] UnionFinderTest.LargerMerges
37: [ OK ] UnionFinderTest.LargerMerges (1 ms)
37: [ RUN ] UnionFinderTest.LongRightMerge
37: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
37: [ RUN ] UnionFinderTest.LongLeftMerge
37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
37: [----------] 5 tests from UnionFinderTest (1 ms total)
37:
37: [----------] 1 test from MappedUnionFinderTest
37: [ RUN ] MappedUnionFinderTest.BasicMerges
37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
37: [----------] 1 test from MappedUnionFinderTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 82 tests from 16 test cases ran. (3706 ms total)
37: [ PASSED ] 82 tests.
37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 3.73 sec
test 38
Start 38: EnergyAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 7 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 1 test from DhdlTest
38: [ RUN ] DhdlTest.ExtractDhdl
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
38: Note: file tpx version 110, software tpx version 119
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
38:
38:
38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
38: [ OK ] DhdlTest.ExtractDhdl (113 ms)
38: [----------] 1 test from DhdlTest (114 ms total)
38:
38: [----------] 1 test from OriresTest
38: [ RUN ] OriresTest.ExtractOrires
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
38: Note: file tpx version 111, software tpx version 119
38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
38: End your selection with 0
38: Selecting all 7 orientation restraints
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
38: [ OK ] OriresTest.ExtractOrires (246 ms)
38: [----------] 1 test from OriresTest (246 ms total)
38:
38: [----------] 3 tests from EnergyTest
38: [ RUN ] EnergyTest.ExtractEnergy
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: [ OK ] EnergyTest.ExtractEnergy (27 ms)
38: [ RUN ] EnergyTest.ExtractEnergyByNumber
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Pres. DC -268.49 3 8.52175 13.2804 (bar)
38: [ OK ] EnergyTest.ExtractEnergyByNumber (26 ms)
38: [ RUN ] EnergyTest.ExtractEnergyMixed
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: [ OK ] EnergyTest.ExtractEnergyMixed (26 ms)
38: [----------] 3 tests from EnergyTest (81 ms total)
38:
38: [----------] 2 tests from ViscosityTest
38: [ RUN ] ViscosityTest.EinsteinViscosity
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosity (52 ms)
38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (49 ms)
38: [----------] 2 tests from ViscosityTest (102 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 7 tests from 4 test cases ran. (544 ms total)
38: [ PASSED ] 7 tests.
38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 0.56 sec
test 39
Start 39: ToolUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 18 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from DumpTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -1252294693
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] DumpTest.WorksWithTpr
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
39: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
39: inputrec:
39: integrator = md
39: tinit = 0
39: dt = 0.001
39: nsteps = 0
39: init-step = 0
39: simulation-part = 1
39: comm-mode = Linear
39: nstcomm = 100
39: bd-fric = 0
39: ld-seed = -1252294693
39: emtol = 10
39: emstep = 0.01
39: niter = 20
39: fcstep = 0
39: nstcgsteep = 1000
39: nbfgscorr = 10
39: rtpi = 0.05
39: nstxout = 0
39: nstvout = 0
39: nstfout = 0
39: nstlog = 1000
39: nstcalcenergy = 100
39: nstenergy = 1000
39: nstxout-compressed = 0
39: compressed-x-precision = 1000
39: cutoff-scheme = Verlet
39: nstlist = 10
39: pbc = xyz
39: periodic-molecules = false
39: verlet-buffer-tolerance = -1
39: rlist = 1.1
39: coulombtype = Cut-off
39: coulomb-modifier = Potential-shift
39: rcoulomb-switch = 0
39: rcoulomb = 1
39: epsilon-r = 1
39: epsilon-rf = inf
39: vdw-type = Cut-off
39: vdw-modifier = Potential-shift
39: rvdw-switch = 0
39: rvdw = 1
39: DispCorr = No
39: table-extension = 1
39: fourierspacing = 0.12
39: fourier-nx = 0
39: fourier-ny = 0
39: fourier-nz = 0
39: pme-order = 4
39: ewald-rtol = 1e-05
39: ewald-rtol-lj = 0.001
39: lj-pme-comb-rule = Geometric
39: ewald-geometry = 0
39: epsilon-surface = 0
39: tcoupl = No
39: nsttcouple = -1
39: nh-chain-length = 0
39: print-nose-hoover-chain-variables = false
39: pcoupl = No
39: pcoupltype = Isotropic
39: nstpcouple = -1
39: tau-p = 1
39: compressibility (3x3):
39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p (3x3):
39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: refcoord-scaling = No
39: posres-com (3):
39: posres-com[0]= 0.00000e+00
39: posres-com[1]= 0.00000e+00
39: posres-com[2]= 0.00000e+00
39: posres-comB (3):
39: posres-comB[0]= 0.00000e+00
39: posres-comB[1]= 0.00000e+00
39: posres-comB[2]= 0.00000e+00
39: QMMM = false
39: QMconstraints = 0
39: QMMMscheme = 0
39: MMChargeScaleFactor = 1
39: qm-opts:
39: ngQM = 0
39: constraint-algorithm = Lincs
39: continuation = false
39: Shake-SOR = false
39: shake-tol = 0.0001
39: lincs-order = 4
39: lincs-iter = 1
39: lincs-warnangle = 30
39: nwall = 0
39: wall-type = 9-3
39: wall-r-linpot = -1
39: wall-atomtype[0] = -1
39: wall-atomtype[1] = -1
39: wall-density[0] = 0
39: wall-density[1] = 0
39: wall-ewald-zfac = 3
39: pull = false
39: awh = false
39: rotation = false
39: interactiveMD = false
39: disre = No
39: disre-weighting = Conservative
39: disre-mixed = false
39: dr-fc = 1000
39: dr-tau = 0
39: nstdisreout = 100
39: orire-fc = 0
39: orire-tau = 0
39: nstorireout = 100
39: free-energy = no
39: cos-acceleration = 0
39: deform (3x3):
39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: simulated-tempering = false
39: swapcoords = no
39: userint1 = 0
39: userint2 = 0
39: userint3 = 0
39: userint4 = 0
39: userreal1 = 0
39: userreal2 = 0
39: userreal3 = 0
39: userreal4 = 0
39: applied-forces:
39: electric-field:
39: x:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: y:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: z:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: density-guided-simulation:
39: active = false
39: group = protein
39: similarity-measure = inner-product
39: atom-spreading-weight = unity
39: force-constant = 1e+09
39: gaussian-transform-spreading-width = 0.2
39: gaussian-transform-spreading-range-in-multiples-of-width = 4
39: reference-density-filename = reference.mrc
39: nst = 1
39: normalize-densities = true
39: adaptive-force-scaling = false
39: adaptive-force-scaling-time-constant = 4
39: grpopts:
39: nrdf: 465
39: ref-t: 0
39: tau-t: 0
39: annealing: No
39: annealing-npoints: 0
39: acc: 0 0 0
39: nfreeze: N N N
39: energygrp-flags[ 0]: 0
39: header:
39: bIr = present
39: bBox = present
39: bTop = present
39: bX = present
39: bV = present
39: bF = not present
39: natoms = 156
39: lambda = 0.000000e+00
39: buffer size = 59422
39: topology:
39: name="First 10 residues from 1AKI"
39: #atoms = 156
39: #molblock = 1
39: molblock (0):
39: moltype = 0 "Protein_chain_B"
39: #molecules = 1
39: #posres_xA = 0
39: #posres_xB = 0
39: bIntermolecularInteractions = false
39: ffparams:
39: atnr=10
39: ntypes=212
39: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
39: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
39: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
39: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
39: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
39: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
39: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
39: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06
39: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
39: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
39: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
39: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
39: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
39: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
39: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
39: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
39: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08
39: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
39: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
39: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
39: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
39: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
39: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
39: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
39: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
39: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05
39: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
39: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
39: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
39: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
39: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
39: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
39: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
39: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
39: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06
39: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
39: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
39: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
39: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
39: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
39: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
39: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
39: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
39: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
39: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
39: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
39: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
39: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
39: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
39: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
39: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
39: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
39: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08
39: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
39: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
39: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
39: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
39: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
39: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
39: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
39: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
39: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08
39: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
39: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
39: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
39: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
39: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
39: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
39: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
39: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
39: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2
39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2
39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2
39: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07
39: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06
39: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06
39: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06
39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
39: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07
39: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06
39: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08
39: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07
39: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06
39: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07
39: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
39: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06
39: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06
39: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06
39: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07
39: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07
39: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07
39: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06
39: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06
39: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08
39: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07
39: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08
39: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06
39: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07
39: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05
39: reppow = 12
39: fudgeQQ = 0.5
39: cmap
39: atomtypes:
39: atomtype[ 0]={atomnumber= 7}
39: atomtype[ 1]={atomnumber= 1}
39: atomtype[ 2]={atomnumber= 6}
39: atomtype[ 3]={atomnumber= 1}
39: atomtype[ 4]={atomnumber= 6}
39: atomtype[ 5]={atomnumber= 8}
39: atomtype[ 6]={atomnumber= 6}
39: atomtype[ 7]={atomnumber= 1}
39: atomtype[ 8]={atomnumber= 6}
39: atomtype[ 9]={atomnumber= 16}
39: moltype (0):
39: name="Protein_chain_B"
39: atoms:
39: atom (156):
39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
39: atom (156):
39: atom[0]={name="N"}
39: atom[1]={name="H1"}
39: atom[2]={name="H2"}
39: atom[3]={name="H3"}
39: atom[4]={name="CA"}
39: atom[5]={name="HA"}
39: atom[6]={name="CB"}
39: atom[7]={name="HB1"}
39: atom[8]={name="HB2"}
39: atom[9]={name="CG"}
39: atom[10]={name="HG1"}
39: atom[11]={name="HG2"}
39: atom[12]={name="CD"}
39: atom[13]={name="HD1"}
39: atom[14]={name="HD2"}
39: atom[15]={name="CE"}
39: atom[16]={name="HE1"}
39: atom[17]={name="HE2"}
39: atom[18]={name="NZ"}
39: atom[19]={name="HZ1"}
39: atom[20]={name="HZ2"}
39: atom[21]={name="HZ3"}
39: atom[22]={name="C"}
39: atom[23]={name="O"}
39: atom[24]={name="N"}
39: atom[25]={name="H"}
39: atom[26]={name="CA"}
39: atom[27]={name="HA"}
39: atom[28]={name="CB"}
39: atom[29]={name="HB"}
39: atom[30]={name="CG1"}
39: atom[31]={name="HG11"}
39: atom[32]={name="HG12"}
39: atom[33]={name="HG13"}
39: atom[34]={name="CG2"}
39: atom[35]={name="HG21"}
39: atom[36]={name="HG22"}
39: atom[37]={name="HG23"}
39: atom[38]={name="C"}
39: atom[39]={name="O"}
39: atom[40]={name="N"}
39: atom[41]={name="H"}
39: atom[42]={name="CA"}
39: atom[43]={name="HA"}
39: atom[44]={name="CB"}
39: atom[45]={name="HB1"}
39: atom[46]={name="HB2"}
39: atom[47]={name="CG"}
39: atom[48]={name="CD1"}
39: atom[49]={name="HD1"}
39: atom[50]={name="CD2"}
39: atom[51]={name="HD2"}
39: atom[52]={name="CE1"}
39: atom[53]={name="HE1"}
39: atom[54]={name="CE2"}
39: atom[55]={name="HE2"}
39: atom[56]={name="CZ"}
39: atom[57]={name="HZ"}
39: atom[58]={name="C"}
39: atom[59]={name="O"}
39: atom[60]={name="N"}
39: atom[61]={name="H"}
39: atom[62]={name="CA"}
39: atom[63]={name="HA1"}
39: atom[64]={name="HA2"}
39: atom[65]={name="C"}
39: atom[66]={name="O"}
39: atom[67]={name="N"}
39: atom[68]={name="H"}
39: atom[69]={name="CA"}
39: atom[70]={name="HA"}
39: atom[71]={name="CB"}
39: atom[72]={name="HB1"}
39: atom[73]={name="HB2"}
39: atom[74]={name="CG"}
39: atom[75]={name="HG1"}
39: atom[76]={name="HG2"}
39: atom[77]={name="CD"}
39: atom[78]={name="HD1"}
39: atom[79]={name="HD2"}
39: atom[80]={name="NE"}
39: atom[81]={name="HE"}
39: atom[82]={name="CZ"}
39: atom[83]={name="NH1"}
39: atom[84]={name="HH11"}
39: atom[85]={name="HH12"}
39: atom[86]={name="NH2"}
39: atom[87]={name="HH21"}
39: atom[88]={name="HH22"}
39: atom[89]={name="C"}
39: atom[90]={name="O"}
39: atom[91]={name="N"}
39: atom[92]={name="H"}
39: atom[93]={name="CA"}
39: atom[94]={name="HA"}
39: atom[95]={name="CB"}
39: atom[96]={name="HB1"}
39: atom[97]={name="HB2"}
39: atom[98]={name="SG"}
39: atom[99]={name="HG"}
39: atom[100]={name="C"}
39: atom[101]={name="O"}
39: atom[102]={name="N"}
39: atom[103]={name="H"}
39: atom[104]={name="CA"}
39: atom[105]={name="HA"}
39: atom[106]={name="CB"}
39: atom[107]={name="HB1"}
39: atom[108]={name="HB2"}
39: atom[109]={name="CG"}
39: atom[110]={name="HG1"}
39: atom[111]={name="HG2"}
39: atom[112]={name="CD"}
39: atom[113]={name="OE1"}
39: atom[114]={name="OE2"}
39: atom[115]={name="C"}
39: atom[116]={name="O"}
39: atom[117]={name="N"}
39: atom[118]={name="H"}
39: atom[119]={name="CA"}
39: atom[120]={name="HA"}
39: atom[121]={name="CB"}
39: atom[122]={name="HB1"}
39: atom[123]={name="HB2"}
39: atom[124]={name="CG"}
39: atom[125]={name="HG"}
39: atom[126]={name="CD1"}
39: atom[127]={name="HD11"}
39: atom[128]={name="HD12"}
39: atom[129]={name="HD13"}
39: atom[130]={name="CD2"}
39: atom[131]={name="HD21"}
39: atom[132]={name="HD22"}
39: atom[133]={name="HD23"}
39: atom[134]={name="C"}
39: atom[135]={name="O"}
39: atom[136]={name="N"}
39: atom[137]={name="H"}
39: atom[138]={name="CA"}
39: atom[139]={name="HA"}
39: atom[140]={name="CB"}
39: atom[141]={name="HB1"}
39: atom[142]={name="HB2"}
39: atom[143]={name="HB3"}
39: atom[144]={name="C"}
39: atom[145]={name="O"}
39: atom[146]={name="N"}
39: atom[147]={name="H"}
39: atom[148]={name="CA"}
39: atom[149]={name="HA"}
39: atom[150]={name="CB"}
39: atom[151]={name="HB1"}
39: atom[152]={name="HB2"}
39: atom[153]={name="HB3"}
39: atom[154]={name="C"}
39: atom[155]={name="O"}
39: type (156):
39: type[0]={name="opls_287",nameB="opls_287"}
39: type[1]={name="opls_290",nameB="opls_290"}
39: type[2]={name="opls_290",nameB="opls_290"}
39: type[3]={name="opls_290",nameB="opls_290"}
39: type[4]={name="opls_293B",nameB="opls_293B"}
39: type[5]={name="opls_140",nameB="opls_140"}
39: type[6]={name="opls_136",nameB="opls_136"}
39: type[7]={name="opls_140",nameB="opls_140"}
39: type[8]={name="opls_140",nameB="opls_140"}
39: type[9]={name="opls_136",nameB="opls_136"}
39: type[10]={name="opls_140",nameB="opls_140"}
39: type[11]={name="opls_140",nameB="opls_140"}
39: type[12]={name="opls_136",nameB="opls_136"}
39: type[13]={name="opls_140",nameB="opls_140"}
39: type[14]={name="opls_140",nameB="opls_140"}
39: type[15]={name="opls_292",nameB="opls_292"}
39: type[16]={name="opls_140",nameB="opls_140"}
39: type[17]={name="opls_140",nameB="opls_140"}
39: type[18]={name="opls_287",nameB="opls_287"}
39: type[19]={name="opls_290",nameB="opls_290"}
39: type[20]={name="opls_290",nameB="opls_290"}
39: type[21]={name="opls_290",nameB="opls_290"}
39: type[22]={name="opls_235",nameB="opls_235"}
39: type[23]={name="opls_236",nameB="opls_236"}
39: type[24]={name="opls_238",nameB="opls_238"}
39: type[25]={name="opls_241",nameB="opls_241"}
39: type[26]={name="opls_224B",nameB="opls_224B"}
39: type[27]={name="opls_140",nameB="opls_140"}
39: type[28]={name="opls_137",nameB="opls_137"}
39: type[29]={name="opls_140",nameB="opls_140"}
39: type[30]={name="opls_135",nameB="opls_135"}
39: type[31]={name="opls_140",nameB="opls_140"}
39: type[32]={name="opls_140",nameB="opls_140"}
39: type[33]={name="opls_140",nameB="opls_140"}
39: type[34]={name="opls_135",nameB="opls_135"}
39: type[35]={name="opls_140",nameB="opls_140"}
39: type[36]={name="opls_140",nameB="opls_140"}
39: type[37]={name="opls_140",nameB="opls_140"}
39: type[38]={name="opls_235",nameB="opls_235"}
39: type[39]={name="opls_236",nameB="opls_236"}
39: type[40]={name="opls_238",nameB="opls_238"}
39: type[41]={name="opls_241",nameB="opls_241"}
39: type[42]={name="opls_224B",nameB="opls_224B"}
39: type[43]={name="opls_140",nameB="opls_140"}
39: type[44]={name="opls_149",nameB="opls_149"}
39: type[45]={name="opls_140",nameB="opls_140"}
39: type[46]={name="opls_140",nameB="opls_140"}
39: type[47]={name="opls_145",nameB="opls_145"}
39: type[48]={name="opls_145",nameB="opls_145"}
39: type[49]={name="opls_146",nameB="opls_146"}
39: type[50]={name="opls_145",nameB="opls_145"}
39: type[51]={name="opls_146",nameB="opls_146"}
39: type[52]={name="opls_145",nameB="opls_145"}
39: type[53]={name="opls_146",nameB="opls_146"}
39: type[54]={name="opls_145",nameB="opls_145"}
39: type[55]={name="opls_146",nameB="opls_146"}
39: type[56]={name="opls_145",nameB="opls_145"}
39: type[57]={name="opls_146",nameB="opls_146"}
39: type[58]={name="opls_235",nameB="opls_235"}
39: type[59]={name="opls_236",nameB="opls_236"}
39: type[60]={name="opls_238",nameB="opls_238"}
39: type[61]={name="opls_241",nameB="opls_241"}
39: type[62]={name="opls_223B",nameB="opls_223B"}
39: type[63]={name="opls_140",nameB="opls_140"}
39: type[64]={name="opls_140",nameB="opls_140"}
39: type[65]={name="opls_235",nameB="opls_235"}
39: type[66]={name="opls_236",nameB="opls_236"}
39: type[67]={name="opls_238",nameB="opls_238"}
39: type[68]={name="opls_241",nameB="opls_241"}
39: type[69]={name="opls_224B",nameB="opls_224B"}
39: type[70]={name="opls_140",nameB="opls_140"}
39: type[71]={name="opls_136",nameB="opls_136"}
39: type[72]={name="opls_140",nameB="opls_140"}
39: type[73]={name="opls_140",nameB="opls_140"}
39: type[74]={name="opls_308",nameB="opls_308"}
39: type[75]={name="opls_140",nameB="opls_140"}
39: type[76]={name="opls_140",nameB="opls_140"}
39: type[77]={name="opls_307",nameB="opls_307"}
39: type[78]={name="opls_140",nameB="opls_140"}
39: type[79]={name="opls_140",nameB="opls_140"}
39: type[80]={name="opls_303",nameB="opls_303"}
39: type[81]={name="opls_304",nameB="opls_304"}
39: type[82]={name="opls_302",nameB="opls_302"}
39: type[83]={name="opls_300",nameB="opls_300"}
39: type[84]={name="opls_301",nameB="opls_301"}
39: type[85]={name="opls_301",nameB="opls_301"}
39: type[86]={name="opls_300",nameB="opls_300"}
39: type[87]={name="opls_301",nameB="opls_301"}
39: type[88]={name="opls_301",nameB="opls_301"}
39: type[89]={name="opls_235",nameB="opls_235"}
39: type[90]={name="opls_236",nameB="opls_236"}
39: type[91]={name="opls_238",nameB="opls_238"}
39: type[92]={name="opls_241",nameB="opls_241"}
39: type[93]={name="opls_224B",nameB="opls_224B"}
39: type[94]={name="opls_140",nameB="opls_140"}
39: type[95]={name="opls_206",nameB="opls_206"}
39: type[96]={name="opls_140",nameB="opls_140"}
39: type[97]={name="opls_140",nameB="opls_140"}
39: type[98]={name="opls_200",nameB="opls_200"}
39: type[99]={name="opls_204",nameB="opls_204"}
39: type[100]={name="opls_235",nameB="opls_235"}
39: type[101]={name="opls_236",nameB="opls_236"}
39: type[102]={name="opls_238",nameB="opls_238"}
39: type[103]={name="opls_241",nameB="opls_241"}
39: type[104]={name="opls_224B",nameB="opls_224B"}
39: type[105]={name="opls_140",nameB="opls_140"}
39: type[106]={name="opls_136",nameB="opls_136"}
39: type[107]={name="opls_140",nameB="opls_140"}
39: type[108]={name="opls_140",nameB="opls_140"}
39: type[109]={name="opls_274",nameB="opls_274"}
39: type[110]={name="opls_140",nameB="opls_140"}
39: type[111]={name="opls_140",nameB="opls_140"}
39: type[112]={name="opls_271",nameB="opls_271"}
39: type[113]={name="opls_272",nameB="opls_272"}
39: type[114]={name="opls_272",nameB="opls_272"}
39: type[115]={name="opls_235",nameB="opls_235"}
39: type[116]={name="opls_236",nameB="opls_236"}
39: type[117]={name="opls_238",nameB="opls_238"}
39: type[118]={name="opls_241",nameB="opls_241"}
39: type[119]={name="opls_224B",nameB="opls_224B"}
39: type[120]={name="opls_140",nameB="opls_140"}
39: type[121]={name="opls_136",nameB="opls_136"}
39: type[122]={name="opls_140",nameB="opls_140"}
39: type[123]={name="opls_140",nameB="opls_140"}
39: type[124]={name="opls_137",nameB="opls_137"}
39: type[125]={name="opls_140",nameB="opls_140"}
39: type[126]={name="opls_135",nameB="opls_135"}
39: type[127]={name="opls_140",nameB="opls_140"}
39: type[128]={name="opls_140",nameB="opls_140"}
39: type[129]={name="opls_140",nameB="opls_140"}
39: type[130]={name="opls_135",nameB="opls_135"}
39: type[131]={name="opls_140",nameB="opls_140"}
39: type[132]={name="opls_140",nameB="opls_140"}
39: type[133]={name="opls_140",nameB="opls_140"}
39: type[134]={name="opls_235",nameB="opls_235"}
39: type[135]={name="opls_236",nameB="opls_236"}
39: type[136]={name="opls_238",nameB="opls_238"}
39: type[137]={name="opls_241",nameB="opls_241"}
39: type[138]={name="opls_224B",nameB="opls_224B"}
39: type[139]={name="opls_140",nameB="opls_140"}
39: type[140]={name="opls_135",nameB="opls_135"}
39: type[141]={name="opls_140",nameB="opls_140"}
39: type[142]={name="opls_140",nameB="opls_140"}
39: type[143]={name="opls_140",nameB="opls_140"}
39: type[144]={name="opls_235",nameB="opls_235"}
39: type[145]={name="opls_236",nameB="opls_236"}
39: type[146]={name="opls_238",nameB="opls_238"}
39: type[147]={name="opls_241",nameB="opls_241"}
39: type[148]={name="opls_224B",nameB="opls_224B"}
39: type[149]={name="opls_140",nameB="opls_140"}
39: type[150]={name="opls_135",nameB="opls_135"}
39: type[151]={name="opls_140",nameB="opls_140"}
39: type[152]={name="opls_140",nameB="opls_140"}
39: type[153]={name="opls_140",nameB="opls_140"}
39: type[154]={name="opls_235",nameB="opls_235"}
39: type[155]={name="opls_236",nameB="opls_236"}
39: residue (10):
39: residue[0]={name="LYS", nr=1, ic=' '}
39: residue[1]={name="VAL", nr=2, ic=' '}
39: residue[2]={name="PHE", nr=3, ic=' '}
39: residue[3]={name="GLY", nr=4, ic=' '}
39: residue[4]={name="ARG", nr=5, ic=' '}
39: residue[5]={name="CYS", nr=6, ic=' '}
39: residue[6]={name="GLU", nr=7, ic=' '}
39: residue[7]={name="LEU", nr=8, ic=' '}
39: residue[8]={name="ALA", nr=9, ic=' '}
39: residue[9]={name="ALA", nr=10, ic=' '}
39: excls:
39: nr=156
39: nra=1828
39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
39: 23, 24, 25, 26}
39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
39: 14, 15, 22, 23, 24}
39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
39: 16, 17, 18, 22}
39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
39: 17, 18, 19, 20, 21}
39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
39: 19, 20, 21}
39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
39: 25, 26, 27, 28, 38}
39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
39: 30, 34, 38, 39, 40}
39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40}
39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
39: 34, 35, 36, 37, 38, 39, 40}
39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40, 41, 42, 43, 44, 58}
39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
39: 45, 46, 47, 58, 59, 60}
39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
39: 48, 50, 58, 59, 60, 61, 62}
39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60}
39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
39: 50, 51, 52, 54, 58, 59, 60}
39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
39: 52, 53, 54, 55, 56, 58}
39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
39: 54, 56, 57}
39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
39: 55, 56, 57}
39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60, 61, 62, 63, 64, 65}
39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
39: 65, 66, 67}
39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
39: 68, 69}
39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
39: 70, 71, 89}
39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
39: 72, 73, 74, 89, 90, 91}
39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
39: 75, 76, 77, 89, 90, 91, 92, 93}
39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
39: 91}
39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
39: 77, 78, 79, 80, 89, 90, 91}
39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
39: 79, 80, 81, 82, 89}
39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
39: 81, 82, 83, 86}
39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
39: 84, 85, 86, 87, 88}
39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
39: 86, 87, 88}
39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
39: 90, 91, 92, 93, 94, 95, 100}
39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
39: 95, 96, 97, 98, 100, 101, 102}
39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
39: 98, 99, 100, 101, 102, 103, 104}
39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102}
39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
39: 100, 101, 102}
39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102, 103, 104, 105, 106, 115}
39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
39: 105, 106, 107, 108, 109, 115, 116, 117}
39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
39: 115}
39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117}
39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 110, 111, 112, 113, 114, 115, 116, 117}
39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 113, 114, 115}
39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117, 118, 119, 120, 121, 134}
39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119}
39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119, 120, 121, 122, 123, 124, 134, 135, 136}
39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
39: 134}
39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136}
39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
39: 136}
39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 127, 128, 129, 130, 131, 132, 133, 134}
39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136, 137, 138, 139, 140, 144}
39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138}
39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138, 139, 140, 141, 142, 143, 144, 145, 146}
39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
39: 144}
39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
39: 141, 142, 143, 144, 145, 146, 147, 148}
39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146, 147, 148, 149, 150, 154}
39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148}
39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148, 149, 150, 151, 152, 153, 154, 155}
39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
39: 154}
39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
39: 151, 152, 153, 154, 155}
39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
39: Bond:
39: nr: 468
39: iatoms:
39: 0 type=100 (BONDS) 0 1
39: 1 type=100 (BONDS) 0 2
39: 2 type=100 (BONDS) 0 3
39: 3 type=101 (BONDS) 0 4
39: 4 type=102 (BONDS) 4 5
39: 5 type=103 (BONDS) 4 6
39: 6 type=104 (BONDS) 4 22
39: 7 type=102 (BONDS) 6 7
39: 8 type=102 (BONDS) 6 8
39: 9 type=103 (BONDS) 6 9
39: 10 type=102 (BONDS) 9 10
39: 11 type=102 (BONDS) 9 11
39: 12 type=103 (BONDS) 9 12
39: 13 type=102 (BONDS) 12 13
39: 14 type=102 (BONDS) 12 14
39: 15 type=103 (BONDS) 12 15
39: 16 type=102 (BONDS) 15 16
39: 17 type=102 (BONDS) 15 17
39: 18 type=101 (BONDS) 15 18
39: 19 type=100 (BONDS) 18 19
39: 20 type=100 (BONDS) 18 20
39: 21 type=100 (BONDS) 18 21
39: 22 type=105 (BONDS) 22 23
39: 23 type=106 (BONDS) 22 24
39: 24 type=100 (BONDS) 24 25
39: 25 type=107 (BONDS) 24 26
39: 26 type=102 (BONDS) 26 27
39: 27 type=103 (BONDS) 26 28
39: 28 type=104 (BONDS) 26 38
39: 29 type=102 (BONDS) 28 29
39: 30 type=103 (BONDS) 28 30
39: 31 type=103 (BONDS) 28 34
39: 32 type=102 (BONDS) 30 31
39: 33 type=102 (BONDS) 30 32
39: 34 type=102 (BONDS) 30 33
39: 35 type=102 (BONDS) 34 35
39: 36 type=102 (BONDS) 34 36
39: 37 type=102 (BONDS) 34 37
39: 38 type=105 (BONDS) 38 39
39: 39 type=106 (BONDS) 38 40
39: 40 type=100 (BONDS) 40 41
39: 41 type=107 (BONDS) 40 42
39: 42 type=102 (BONDS) 42 43
39: 43 type=103 (BONDS) 42 44
39: 44 type=104 (BONDS) 42 58
39: 45 type=102 (BONDS) 44 45
39: 46 type=102 (BONDS) 44 46
39: 47 type=108 (BONDS) 44 47
39: 48 type=109 (BONDS) 47 48
39: 49 type=109 (BONDS) 47 50
39: 50 type=110 (BONDS) 48 49
39: 51 type=109 (BONDS) 48 52
39: 52 type=110 (BONDS) 50 51
39: 53 type=109 (BONDS) 50 54
39: 54 type=110 (BONDS) 52 53
39: 55 type=109 (BONDS) 52 56
39: 56 type=110 (BONDS) 54 55
39: 57 type=109 (BONDS) 54 56
39: 58 type=110 (BONDS) 56 57
39: 59 type=105 (BONDS) 58 59
39: 60 type=106 (BONDS) 58 60
39: 61 type=100 (BONDS) 60 61
39: 62 type=107 (BONDS) 60 62
39: 63 type=102 (BONDS) 62 63
39: 64 type=102 (BONDS) 62 64
39: 65 type=104 (BONDS) 62 65
39: 66 type=105 (BONDS) 65 66
39: 67 type=106 (BONDS) 65 67
39: 68 type=100 (BONDS) 67 68
39: 69 type=107 (BONDS) 67 69
39: 70 type=102 (BONDS) 69 70
39: 71 type=103 (BONDS) 69 71
39: 72 type=104 (BONDS) 69 89
39: 73 type=102 (BONDS) 71 72
39: 74 type=102 (BONDS) 71 73
39: 75 type=103 (BONDS) 71 74
39: 76 type=102 (BONDS) 74 75
39: 77 type=102 (BONDS) 74 76
39: 78 type=103 (BONDS) 74 77
39: 79 type=102 (BONDS) 77 78
39: 80 type=102 (BONDS) 77 79
39: 81 type=111 (BONDS) 77 80
39: 82 type=100 (BONDS) 80 81
39: 83 type=112 (BONDS) 80 82
39: 84 type=112 (BONDS) 82 83
39: 85 type=112 (BONDS) 82 86
39: 86 type=100 (BONDS) 83 84
39: 87 type=100 (BONDS) 83 85
39: 88 type=100 (BONDS) 86 87
39: 89 type=100 (BONDS) 86 88
39: 90 type=105 (BONDS) 89 90
39: 91 type=106 (BONDS) 89 91
39: 92 type=100 (BONDS) 91 92
39: 93 type=107 (BONDS) 91 93
39: 94 type=102 (BONDS) 93 94
39: 95 type=103 (BONDS) 93 95
39: 96 type=104 (BONDS) 93 100
39: 97 type=102 (BONDS) 95 96
39: 98 type=102 (BONDS) 95 97
39: 99 type=113 (BONDS) 95 98
39: 100 type=114 (BONDS) 98 99
39: 101 type=105 (BONDS) 100 101
39: 102 type=106 (BONDS) 100 102
39: 103 type=100 (BONDS) 102 103
39: 104 type=107 (BONDS) 102 104
39: 105 type=102 (BONDS) 104 105
39: 106 type=103 (BONDS) 104 106
39: 107 type=104 (BONDS) 104 115
39: 108 type=102 (BONDS) 106 107
39: 109 type=102 (BONDS) 106 108
39: 110 type=103 (BONDS) 106 109
39: 111 type=102 (BONDS) 109 110
39: 112 type=102 (BONDS) 109 111
39: 113 type=104 (BONDS) 109 112
39: 114 type=115 (BONDS) 112 113
39: 115 type=115 (BONDS) 112 114
39: 116 type=105 (BONDS) 115 116
39: 117 type=106 (BONDS) 115 117
39: 118 type=100 (BONDS) 117 118
39: 119 type=107 (BONDS) 117 119
39: 120 type=102 (BONDS) 119 120
39: 121 type=103 (BONDS) 119 121
39: 122 type=104 (BONDS) 119 134
39: 123 type=102 (BONDS) 121 122
39: 124 type=102 (BONDS) 121 123
39: 125 type=103 (BONDS) 121 124
39: 126 type=102 (BONDS) 124 125
39: 127 type=103 (BONDS) 124 126
39: 128 type=103 (BONDS) 124 130
39: 129 type=102 (BONDS) 126 127
39: 130 type=102 (BONDS) 126 128
39: 131 type=102 (BONDS) 126 129
39: 132 type=102 (BONDS) 130 131
39: 133 type=102 (BONDS) 130 132
39: 134 type=102 (BONDS) 130 133
39: 135 type=105 (BONDS) 134 135
39: 136 type=106 (BONDS) 134 136
39: 137 type=100 (BONDS) 136 137
39: 138 type=107 (BONDS) 136 138
39: 139 type=102 (BONDS) 138 139
39: 140 type=103 (BONDS) 138 140
39: 141 type=104 (BONDS) 138 144
39: 142 type=102 (BONDS) 140 141
39: 143 type=102 (BONDS) 140 142
39: 144 type=102 (BONDS) 140 143
39: 145 type=105 (BONDS) 144 145
39: 146 type=106 (BONDS) 144 146
39: 147 type=100 (BONDS) 146 147
39: 148 type=107 (BONDS) 146 148
39: 149 type=102 (BONDS) 148 149
39: 150 type=103 (BONDS) 148 150
39: 151 type=104 (BONDS) 148 154
39: 152 type=102 (BONDS) 150 151
39: 153 type=102 (BONDS) 150 152
39: 154 type=102 (BONDS) 150 153
39: 155 type=105 (BONDS) 154 155
39: G96Bond:
39: nr: 0
39: Morse:
39: nr: 0
39: Cubic Bonds:
39: nr: 0
39: Connect Bonds:
39: nr: 0
39: Harmonic Pot.:
39: nr: 0
39: FENE Bonds:
39: nr: 0
39: Tab. Bonds:
39: nr: 0
39: Tab. Bonds NC:
39: nr: 0
39: Restraint Pot.:
39: nr: 0
39: Angle:
39: nr: 1124
39: iatoms:
39: 0 type=116 (ANGLES) 1 0 2
39: 1 type=116 (ANGLES) 1 0 3
39: 2 type=116 (ANGLES) 1 0 4
39: 3 type=116 (ANGLES) 2 0 3
39: 4 type=116 (ANGLES) 2 0 4
39: 5 type=116 (ANGLES) 3 0 4
39: 6 type=116 (ANGLES) 0 4 5
39: 7 type=117 (ANGLES) 0 4 6
39: 8 type=117 (ANGLES) 0 4 22
39: 9 type=118 (ANGLES) 5 4 6
39: 10 type=116 (ANGLES) 5 4 22
39: 11 type=119 (ANGLES) 6 4 22
39: 12 type=118 (ANGLES) 4 6 7
39: 13 type=118 (ANGLES) 4 6 8
39: 14 type=120 (ANGLES) 4 6 9
39: 15 type=121 (ANGLES) 7 6 8
39: 16 type=118 (ANGLES) 7 6 9
39: 17 type=118 (ANGLES) 8 6 9
39: 18 type=118 (ANGLES) 6 9 10
39: 19 type=118 (ANGLES) 6 9 11
39: 20 type=120 (ANGLES) 6 9 12
39: 21 type=121 (ANGLES) 10 9 11
39: 22 type=118 (ANGLES) 10 9 12
39: 23 type=118 (ANGLES) 11 9 12
39: 24 type=118 (ANGLES) 9 12 13
39: 25 type=118 (ANGLES) 9 12 14
39: 26 type=120 (ANGLES) 9 12 15
39: 27 type=121 (ANGLES) 13 12 14
39: 28 type=118 (ANGLES) 13 12 15
39: 29 type=118 (ANGLES) 14 12 15
39: 30 type=118 (ANGLES) 12 15 16
39: 31 type=118 (ANGLES) 12 15 17
39: 32 type=117 (ANGLES) 12 15 18
39: 33 type=121 (ANGLES) 16 15 17
39: 34 type=116 (ANGLES) 16 15 18
39: 35 type=116 (ANGLES) 17 15 18
39: 36 type=116 (ANGLES) 15 18 19
39: 37 type=116 (ANGLES) 15 18 20
39: 38 type=116 (ANGLES) 15 18 21
39: 39 type=116 (ANGLES) 19 18 20
39: 40 type=116 (ANGLES) 19 18 21
39: 41 type=116 (ANGLES) 20 18 21
39: 42 type=122 (ANGLES) 4 22 23
39: 43 type=123 (ANGLES) 4 22 24
39: 44 type=124 (ANGLES) 23 22 24
39: 45 type=125 (ANGLES) 22 24 25
39: 46 type=126 (ANGLES) 22 24 26
39: 47 type=127 (ANGLES) 25 24 26
39: 48 type=116 (ANGLES) 24 26 27
39: 49 type=128 (ANGLES) 24 26 28
39: 50 type=129 (ANGLES) 24 26 38
39: 51 type=118 (ANGLES) 27 26 28
39: 52 type=116 (ANGLES) 27 26 38
39: 53 type=119 (ANGLES) 28 26 38
39: 54 type=118 (ANGLES) 26 28 29
39: 55 type=120 (ANGLES) 26 28 30
39: 56 type=120 (ANGLES) 26 28 34
39: 57 type=118 (ANGLES) 29 28 30
39: 58 type=118 (ANGLES) 29 28 34
39: 59 type=120 (ANGLES) 30 28 34
39: 60 type=118 (ANGLES) 28 30 31
39: 61 type=118 (ANGLES) 28 30 32
39: 62 type=118 (ANGLES) 28 30 33
39: 63 type=121 (ANGLES) 31 30 32
39: 64 type=121 (ANGLES) 31 30 33
39: 65 type=121 (ANGLES) 32 30 33
39: 66 type=118 (ANGLES) 28 34 35
39: 67 type=118 (ANGLES) 28 34 36
39: 68 type=118 (ANGLES) 28 34 37
39: 69 type=121 (ANGLES) 35 34 36
39: 70 type=121 (ANGLES) 35 34 37
39: 71 type=121 (ANGLES) 36 34 37
39: 72 type=122 (ANGLES) 26 38 39
39: 73 type=123 (ANGLES) 26 38 40
39: 74 type=124 (ANGLES) 39 38 40
39: 75 type=125 (ANGLES) 38 40 41
39: 76 type=126 (ANGLES) 38 40 42
39: 77 type=127 (ANGLES) 41 40 42
39: 78 type=116 (ANGLES) 40 42 43
39: 79 type=128 (ANGLES) 40 42 44
39: 80 type=129 (ANGLES) 40 42 58
39: 81 type=118 (ANGLES) 43 42 44
39: 82 type=116 (ANGLES) 43 42 58
39: 83 type=119 (ANGLES) 44 42 58
39: 84 type=118 (ANGLES) 42 44 45
39: 85 type=118 (ANGLES) 42 44 46
39: 86 type=130 (ANGLES) 42 44 47
39: 87 type=121 (ANGLES) 45 44 46
39: 88 type=116 (ANGLES) 45 44 47
39: 89 type=116 (ANGLES) 46 44 47
39: 90 type=131 (ANGLES) 44 47 48
39: 91 type=131 (ANGLES) 44 47 50
39: 92 type=132 (ANGLES) 48 47 50
39: 93 type=133 (ANGLES) 47 48 49
39: 94 type=132 (ANGLES) 47 48 52
39: 95 type=133 (ANGLES) 49 48 52
39: 96 type=133 (ANGLES) 47 50 51
39: 97 type=132 (ANGLES) 47 50 54
39: 98 type=133 (ANGLES) 51 50 54
39: 99 type=133 (ANGLES) 48 52 53
39: 100 type=132 (ANGLES) 48 52 56
39: 101 type=133 (ANGLES) 53 52 56
39: 102 type=133 (ANGLES) 50 54 55
39: 103 type=132 (ANGLES) 50 54 56
39: 104 type=133 (ANGLES) 55 54 56
39: 105 type=132 (ANGLES) 52 56 54
39: 106 type=133 (ANGLES) 52 56 57
39: 107 type=133 (ANGLES) 54 56 57
39: 108 type=122 (ANGLES) 42 58 59
39: 109 type=123 (ANGLES) 42 58 60
39: 110 type=124 (ANGLES) 59 58 60
39: 111 type=125 (ANGLES) 58 60 61
39: 112 type=126 (ANGLES) 58 60 62
39: 113 type=127 (ANGLES) 61 60 62
39: 114 type=116 (ANGLES) 60 62 63
39: 115 type=116 (ANGLES) 60 62 64
39: 116 type=129 (ANGLES) 60 62 65
39: 117 type=121 (ANGLES) 63 62 64
39: 118 type=116 (ANGLES) 63 62 65
39: 119 type=116 (ANGLES) 64 62 65
39: 120 type=122 (ANGLES) 62 65 66
39: 121 type=123 (ANGLES) 62 65 67
39: 122 type=124 (ANGLES) 66 65 67
39: 123 type=125 (ANGLES) 65 67 68
39: 124 type=126 (ANGLES) 65 67 69
39: 125 type=127 (ANGLES) 68 67 69
39: 126 type=116 (ANGLES) 67 69 70
39: 127 type=128 (ANGLES) 67 69 71
39: 128 type=129 (ANGLES) 67 69 89
39: 129 type=118 (ANGLES) 70 69 71
39: 130 type=116 (ANGLES) 70 69 89
39: 131 type=119 (ANGLES) 71 69 89
39: 132 type=118 (ANGLES) 69 71 72
39: 133 type=118 (ANGLES) 69 71 73
39: 134 type=120 (ANGLES) 69 71 74
39: 135 type=121 (ANGLES) 72 71 73
39: 136 type=118 (ANGLES) 72 71 74
39: 137 type=118 (ANGLES) 73 71 74
39: 138 type=118 (ANGLES) 71 74 75
39: 139 type=118 (ANGLES) 71 74 76
39: 140 type=120 (ANGLES) 71 74 77
39: 141 type=121 (ANGLES) 75 74 76
39: 142 type=118 (ANGLES) 75 74 77
39: 143 type=118 (ANGLES) 76 74 77
39: 144 type=118 (ANGLES) 74 77 78
39: 145 type=118 (ANGLES) 74 77 79
39: 146 type=117 (ANGLES) 74 77 80
39: 147 type=121 (ANGLES) 78 77 79
39: 148 type=116 (ANGLES) 78 77 80
39: 149 type=116 (ANGLES) 79 77 80
39: 150 type=134 (ANGLES) 77 80 81
39: 151 type=135 (ANGLES) 77 80 82
39: 152 type=133 (ANGLES) 81 80 82
39: 153 type=131 (ANGLES) 80 82 83
39: 154 type=131 (ANGLES) 80 82 86
39: 155 type=131 (ANGLES) 83 82 86
39: 156 type=133 (ANGLES) 82 83 84
39: 157 type=133 (ANGLES) 82 83 85
39: 158 type=133 (ANGLES) 84 83 85
39: 159 type=133 (ANGLES) 82 86 87
39: 160 type=133 (ANGLES) 82 86 88
39: 161 type=133 (ANGLES) 87 86 88
39: 162 type=122 (ANGLES) 69 89 90
39: 163 type=123 (ANGLES) 69 89 91
39: 164 type=124 (ANGLES) 90 89 91
39: 165 type=125 (ANGLES) 89 91 92
39: 166 type=126 (ANGLES) 89 91 93
39: 167 type=127 (ANGLES) 92 91 93
39: 168 type=116 (ANGLES) 91 93 94
39: 169 type=128 (ANGLES) 91 93 95
39: 170 type=129 (ANGLES) 91 93 100
39: 171 type=118 (ANGLES) 94 93 95
39: 172 type=116 (ANGLES) 94 93 100
39: 173 type=119 (ANGLES) 95 93 100
39: 174 type=118 (ANGLES) 93 95 96
39: 175 type=118 (ANGLES) 93 95 97
39: 176 type=136 (ANGLES) 93 95 98
39: 177 type=121 (ANGLES) 96 95 97
39: 178 type=116 (ANGLES) 96 95 98
39: 179 type=116 (ANGLES) 97 95 98
39: 180 type=137 (ANGLES) 95 98 99
39: 181 type=122 (ANGLES) 93 100 101
39: 182 type=123 (ANGLES) 93 100 102
39: 183 type=124 (ANGLES) 101 100 102
39: 184 type=125 (ANGLES) 100 102 103
39: 185 type=126 (ANGLES) 100 102 104
39: 186 type=127 (ANGLES) 103 102 104
39: 187 type=116 (ANGLES) 102 104 105
39: 188 type=128 (ANGLES) 102 104 106
39: 189 type=129 (ANGLES) 102 104 115
39: 190 type=118 (ANGLES) 105 104 106
39: 191 type=116 (ANGLES) 105 104 115
39: 192 type=119 (ANGLES) 106 104 115
39: 193 type=118 (ANGLES) 104 106 107
39: 194 type=118 (ANGLES) 104 106 108
39: 195 type=120 (ANGLES) 104 106 109
39: 196 type=121 (ANGLES) 107 106 108
39: 197 type=118 (ANGLES) 107 106 109
39: 198 type=118 (ANGLES) 108 106 109
39: 199 type=118 (ANGLES) 106 109 110
39: 200 type=118 (ANGLES) 106 109 111
39: 201 type=119 (ANGLES) 106 109 112
39: 202 type=121 (ANGLES) 110 109 111
39: 203 type=116 (ANGLES) 110 109 112
39: 204 type=116 (ANGLES) 111 109 112
39: 205 type=138 (ANGLES) 109 112 113
39: 206 type=138 (ANGLES) 109 112 114
39: 207 type=139 (ANGLES) 113 112 114
39: 208 type=122 (ANGLES) 104 115 116
39: 209 type=123 (ANGLES) 104 115 117
39: 210 type=124 (ANGLES) 116 115 117
39: 211 type=125 (ANGLES) 115 117 118
39: 212 type=126 (ANGLES) 115 117 119
39: 213 type=127 (ANGLES) 118 117 119
39: 214 type=116 (ANGLES) 117 119 120
39: 215 type=128 (ANGLES) 117 119 121
39: 216 type=129 (ANGLES) 117 119 134
39: 217 type=118 (ANGLES) 120 119 121
39: 218 type=116 (ANGLES) 120 119 134
39: 219 type=119 (ANGLES) 121 119 134
39: 220 type=118 (ANGLES) 119 121 122
39: 221 type=118 (ANGLES) 119 121 123
39: 222 type=120 (ANGLES) 119 121 124
39: 223 type=121 (ANGLES) 122 121 123
39: 224 type=118 (ANGLES) 122 121 124
39: 225 type=118 (ANGLES) 123 121 124
39: 226 type=118 (ANGLES) 121 124 125
39: 227 type=120 (ANGLES) 121 124 126
39: 228 type=120 (ANGLES) 121 124 130
39: 229 type=118 (ANGLES) 125 124 126
39: 230 type=118 (ANGLES) 125 124 130
39: 231 type=120 (ANGLES) 126 124 130
39: 232 type=118 (ANGLES) 124 126 127
39: 233 type=118 (ANGLES) 124 126 128
39: 234 type=118 (ANGLES) 124 126 129
39: 235 type=121 (ANGLES) 127 126 128
39: 236 type=121 (ANGLES) 127 126 129
39: 237 type=121 (ANGLES) 128 126 129
39: 238 type=118 (ANGLES) 124 130 131
39: 239 type=118 (ANGLES) 124 130 132
39: 240 type=118 (ANGLES) 124 130 133
39: 241 type=121 (ANGLES) 131 130 132
39: 242 type=121 (ANGLES) 131 130 133
39: 243 type=121 (ANGLES) 132 130 133
39: 244 type=122 (ANGLES) 119 134 135
39: 245 type=123 (ANGLES) 119 134 136
39: 246 type=124 (ANGLES) 135 134 136
39: 247 type=125 (ANGLES) 134 136 137
39: 248 type=126 (ANGLES) 134 136 138
39: 249 type=127 (ANGLES) 137 136 138
39: 250 type=116 (ANGLES) 136 138 139
39: 251 type=128 (ANGLES) 136 138 140
39: 252 type=129 (ANGLES) 136 138 144
39: 253 type=118 (ANGLES) 139 138 140
39: 254 type=116 (ANGLES) 139 138 144
39: 255 type=119 (ANGLES) 140 138 144
39: 256 type=118 (ANGLES) 138 140 141
39: 257 type=118 (ANGLES) 138 140 142
39: 258 type=118 (ANGLES) 138 140 143
39: 259 type=121 (ANGLES) 141 140 142
39: 260 type=121 (ANGLES) 141 140 143
39: 261 type=121 (ANGLES) 142 140 143
39: 262 type=122 (ANGLES) 138 144 145
39: 263 type=123 (ANGLES) 138 144 146
39: 264 type=124 (ANGLES) 145 144 146
39: 265 type=125 (ANGLES) 144 146 147
39: 266 type=126 (ANGLES) 144 146 148
39: 267 type=127 (ANGLES) 147 146 148
39: 268 type=116 (ANGLES) 146 148 149
39: 269 type=128 (ANGLES) 146 148 150
39: 270 type=129 (ANGLES) 146 148 154
39: 271 type=118 (ANGLES) 149 148 150
39: 272 type=116 (ANGLES) 149 148 154
39: 273 type=119 (ANGLES) 150 148 154
39: 274 type=118 (ANGLES) 148 150 151
39: 275 type=118 (ANGLES) 148 150 152
39: 276 type=118 (ANGLES) 148 150 153
39: 277 type=121 (ANGLES) 151 150 152
39: 278 type=121 (ANGLES) 151 150 153
39: 279 type=121 (ANGLES) 152 150 153
39: 280 type=122 (ANGLES) 148 154 155
39: G96Angle:
39: nr: 0
39: Restricted Angles:
39: nr: 0
39: Lin. Angle:
39: nr: 0
39: Bond-Cross:
39: nr: 0
39: BA-Cross:
39: nr: 0
39: U-B:
39: nr: 0
39: Quartic Angles:
39: nr: 0
39: Tab. Angles:
39: nr: 0
39: Proper Dih.:
39: nr: 145
39: iatoms:
39: 0 type=140 (PDIHS) 4 24 22 23
39: 1 type=141 (PDIHS) 22 26 24 25
39: 2 type=140 (PDIHS) 26 40 38 39
39: 3 type=141 (PDIHS) 38 42 40 41
39: 4 type=140 (PDIHS) 42 60 58 59
39: 5 type=142 (PDIHS) 44 47 50 48
39: 6 type=142 (PDIHS) 47 52 48 49
39: 7 type=142 (PDIHS) 47 54 50 51
39: 8 type=142 (PDIHS) 48 56 52 53
39: 9 type=142 (PDIHS) 50 56 54 55
39: 10 type=142 (PDIHS) 52 54 56 57
39: 11 type=141 (PDIHS) 58 62 60 61
39: 12 type=140 (PDIHS) 62 67 65 66
39: 13 type=141 (PDIHS) 65 69 67 68
39: 14 type=140 (PDIHS) 69 91 89 90
39: 15 type=141 (PDIHS) 77 82 80 81
39: 16 type=140 (PDIHS) 80 83 82 86
39: 17 type=141 (PDIHS) 82 84 83 85
39: 18 type=141 (PDIHS) 82 87 86 88
39: 19 type=141 (PDIHS) 89 93 91 92
39: 20 type=140 (PDIHS) 93 102 100 101
39: 21 type=141 (PDIHS) 100 104 102 103
39: 22 type=140 (PDIHS) 104 117 115 116
39: 23 type=140 (PDIHS) 109 113 112 114
39: 24 type=141 (PDIHS) 115 119 117 118
39: 25 type=140 (PDIHS) 119 136 134 135
39: 26 type=141 (PDIHS) 134 138 136 137
39: 27 type=140 (PDIHS) 138 146 144 145
39: 28 type=141 (PDIHS) 144 148 146 147
39: Ryckaert-Bell.:
39: nr: 1565
39: iatoms:
39: 0 type=143 (RBDIHS) 1 0 4 5
39: 1 type=144 (RBDIHS) 1 0 4 6
39: 2 type=144 (RBDIHS) 1 0 4 22
39: 3 type=143 (RBDIHS) 2 0 4 5
39: 4 type=144 (RBDIHS) 2 0 4 6
39: 5 type=144 (RBDIHS) 2 0 4 22
39: 6 type=143 (RBDIHS) 3 0 4 5
39: 7 type=144 (RBDIHS) 3 0 4 6
39: 8 type=144 (RBDIHS) 3 0 4 22
39: 9 type=145 (RBDIHS) 0 4 6 9
39: 10 type=146 (RBDIHS) 22 4 6 9
39: 11 type=147 (RBDIHS) 0 4 6 7
39: 12 type=147 (RBDIHS) 0 4 6 8
39: 13 type=148 (RBDIHS) 5 4 6 7
39: 14 type=148 (RBDIHS) 5 4 6 8
39: 15 type=148 (RBDIHS) 5 4 6 9
39: 16 type=149 (RBDIHS) 22 4 6 7
39: 17 type=149 (RBDIHS) 22 4 6 8
39: 18 type=150 (RBDIHS) 0 4 22 24
39: 19 type=151 (RBDIHS) 6 4 22 24
39: 20 type=148 (RBDIHS) 4 6 9 10
39: 21 type=148 (RBDIHS) 4 6 9 11
39: 22 type=152 (RBDIHS) 4 6 9 12
39: 23 type=148 (RBDIHS) 7 6 9 10
39: 24 type=148 (RBDIHS) 7 6 9 11
39: 25 type=148 (RBDIHS) 7 6 9 12
39: 26 type=148 (RBDIHS) 8 6 9 10
39: 27 type=148 (RBDIHS) 8 6 9 11
39: 28 type=148 (RBDIHS) 8 6 9 12
39: 29 type=148 (RBDIHS) 6 9 12 13
39: 30 type=148 (RBDIHS) 6 9 12 14
39: 31 type=152 (RBDIHS) 6 9 12 15
39: 32 type=148 (RBDIHS) 10 9 12 13
39: 33 type=148 (RBDIHS) 10 9 12 14
39: 34 type=148 (RBDIHS) 10 9 12 15
39: 35 type=148 (RBDIHS) 11 9 12 13
39: 36 type=148 (RBDIHS) 11 9 12 14
39: 37 type=148 (RBDIHS) 11 9 12 15
39: 38 type=148 (RBDIHS) 9 12 15 16
39: 39 type=148 (RBDIHS) 9 12 15 17
39: 40 type=153 (RBDIHS) 9 12 15 18
39: 41 type=148 (RBDIHS) 13 12 15 16
39: 42 type=148 (RBDIHS) 13 12 15 17
39: 43 type=154 (RBDIHS) 13 12 15 18
39: 44 type=148 (RBDIHS) 14 12 15 16
39: 45 type=148 (RBDIHS) 14 12 15 17
39: 46 type=154 (RBDIHS) 14 12 15 18
39: 47 type=144 (RBDIHS) 12 15 18 19
39: 48 type=144 (RBDIHS) 12 15 18 20
39: 49 type=144 (RBDIHS) 12 15 18 21
39: 50 type=143 (RBDIHS) 16 15 18 19
39: 51 type=143 (RBDIHS) 16 15 18 20
39: 52 type=143 (RBDIHS) 16 15 18 21
39: 53 type=143 (RBDIHS) 17 15 18 19
39: 54 type=143 (RBDIHS) 17 15 18 20
39: 55 type=143 (RBDIHS) 17 15 18 21
39: 56 type=155 (RBDIHS) 4 22 24 25
39: 57 type=156 (RBDIHS) 4 22 24 26
39: 58 type=155 (RBDIHS) 23 22 24 25
39: 59 type=157 (RBDIHS) 23 22 24 26
39: 60 type=158 (RBDIHS) 22 24 26 28
39: 61 type=159 (RBDIHS) 22 24 26 38
39: 62 type=160 (RBDIHS) 24 26 28 30
39: 63 type=160 (RBDIHS) 24 26 28 34
39: 64 type=161 (RBDIHS) 38 26 28 30
39: 65 type=161 (RBDIHS) 38 26 28 34
39: 66 type=147 (RBDIHS) 24 26 28 29
39: 67 type=148 (RBDIHS) 27 26 28 29
39: 68 type=148 (RBDIHS) 27 26 28 30
39: 69 type=148 (RBDIHS) 27 26 28 34
39: 70 type=149 (RBDIHS) 38 26 28 29
39: 71 type=150 (RBDIHS) 24 26 38 40
39: 72 type=151 (RBDIHS) 28 26 38 40
39: 73 type=148 (RBDIHS) 26 28 30 31
39: 74 type=148 (RBDIHS) 26 28 30 32
39: 75 type=148 (RBDIHS) 26 28 30 33
39: 76 type=148 (RBDIHS) 29 28 30 31
39: 77 type=148 (RBDIHS) 29 28 30 32
39: 78 type=148 (RBDIHS) 29 28 30 33
39: 79 type=148 (RBDIHS) 34 28 30 31
39: 80 type=148 (RBDIHS) 34 28 30 32
39: 81 type=148 (RBDIHS) 34 28 30 33
39: 82 type=148 (RBDIHS) 26 28 34 35
39: 83 type=148 (RBDIHS) 26 28 34 36
39: 84 type=148 (RBDIHS) 26 28 34 37
39: 85 type=148 (RBDIHS) 29 28 34 35
39: 86 type=148 (RBDIHS) 29 28 34 36
39: 87 type=148 (RBDIHS) 29 28 34 37
39: 88 type=148 (RBDIHS) 30 28 34 35
39: 89 type=148 (RBDIHS) 30 28 34 36
39: 90 type=148 (RBDIHS) 30 28 34 37
39: 91 type=155 (RBDIHS) 26 38 40 41
39: 92 type=156 (RBDIHS) 26 38 40 42
39: 93 type=155 (RBDIHS) 39 38 40 41
39: 94 type=157 (RBDIHS) 39 38 40 42
39: 95 type=158 (RBDIHS) 38 40 42 44
39: 96 type=159 (RBDIHS) 38 40 42 58
39: 97 type=147 (RBDIHS) 40 42 44 45
39: 98 type=147 (RBDIHS) 40 42 44 46
39: 99 type=162 (RBDIHS) 40 42 44 47
39: 100 type=148 (RBDIHS) 43 42 44 45
39: 101 type=148 (RBDIHS) 43 42 44 46
39: 102 type=163 (RBDIHS) 43 42 44 47
39: 103 type=149 (RBDIHS) 58 42 44 45
39: 104 type=149 (RBDIHS) 58 42 44 46
39: 105 type=164 (RBDIHS) 58 42 44 47
39: 106 type=150 (RBDIHS) 40 42 58 60
39: 107 type=151 (RBDIHS) 44 42 58 60
39: 108 type=165 (RBDIHS) 44 47 48 49
39: 109 type=165 (RBDIHS) 44 47 48 52
39: 110 type=165 (RBDIHS) 50 47 48 49
39: 111 type=165 (RBDIHS) 50 47 48 52
39: 112 type=165 (RBDIHS) 44 47 50 51
39: 113 type=165 (RBDIHS) 44 47 50 54
39: 114 type=165 (RBDIHS) 48 47 50 51
39: 115 type=165 (RBDIHS) 48 47 50 54
39: 116 type=165 (RBDIHS) 47 48 52 53
39: 117 type=165 (RBDIHS) 47 48 52 56
39: 118 type=165 (RBDIHS) 49 48 52 53
39: 119 type=165 (RBDIHS) 49 48 52 56
39: 120 type=165 (RBDIHS) 47 50 54 55
39: 121 type=165 (RBDIHS) 47 50 54 56
39: 122 type=165 (RBDIHS) 51 50 54 55
39: 123 type=165 (RBDIHS) 51 50 54 56
39: 124 type=165 (RBDIHS) 48 52 56 54
39: 125 type=165 (RBDIHS) 48 52 56 57
39: 126 type=165 (RBDIHS) 53 52 56 54
39: 127 type=165 (RBDIHS) 53 52 56 57
39: 128 type=165 (RBDIHS) 50 54 56 52
39: 129 type=165 (RBDIHS) 50 54 56 57
39: 130 type=165 (RBDIHS) 55 54 56 52
39: 131 type=165 (RBDIHS) 55 54 56 57
39: 132 type=155 (RBDIHS) 42 58 60 61
39: 133 type=156 (RBDIHS) 42 58 60 62
39: 134 type=155 (RBDIHS) 59 58 60 61
39: 135 type=157 (RBDIHS) 59 58 60 62
39: 136 type=159 (RBDIHS) 58 60 62 65
39: 137 type=150 (RBDIHS) 60 62 65 67
39: 138 type=155 (RBDIHS) 62 65 67 68
39: 139 type=156 (RBDIHS) 62 65 67 69
39: 140 type=155 (RBDIHS) 66 65 67 68
39: 141 type=157 (RBDIHS) 66 65 67 69
39: 142 type=158 (RBDIHS) 65 67 69 71
39: 143 type=159 (RBDIHS) 65 67 69 89
39: 144 type=166 (RBDIHS) 67 69 71 74
39: 145 type=167 (RBDIHS) 89 69 71 74
39: 146 type=147 (RBDIHS) 67 69 71 72
39: 147 type=147 (RBDIHS) 67 69 71 73
39: 148 type=148 (RBDIHS) 70 69 71 72
39: 149 type=148 (RBDIHS) 70 69 71 73
39: 150 type=148 (RBDIHS) 70 69 71 74
39: 151 type=149 (RBDIHS) 89 69 71 72
39: 152 type=149 (RBDIHS) 89 69 71 73
39: 153 type=150 (RBDIHS) 67 69 89 91
39: 154 type=151 (RBDIHS) 71 69 89 91
39: 155 type=148 (RBDIHS) 69 71 74 75
39: 156 type=148 (RBDIHS) 69 71 74 76
39: 157 type=152 (RBDIHS) 69 71 74 77
39: 158 type=148 (RBDIHS) 72 71 74 75
39: 159 type=148 (RBDIHS) 72 71 74 76
39: 160 type=148 (RBDIHS) 72 71 74 77
39: 161 type=148 (RBDIHS) 73 71 74 75
39: 162 type=148 (RBDIHS) 73 71 74 76
39: 163 type=148 (RBDIHS) 73 71 74 77
39: 164 type=148 (RBDIHS) 71 74 77 78
39: 165 type=148 (RBDIHS) 71 74 77 79
39: 166 type=153 (RBDIHS) 71 74 77 80
39: 167 type=148 (RBDIHS) 75 74 77 78
39: 168 type=148 (RBDIHS) 75 74 77 79
39: 169 type=168 (RBDIHS) 75 74 77 80
39: 170 type=148 (RBDIHS) 76 74 77 78
39: 171 type=148 (RBDIHS) 76 74 77 79
39: 172 type=168 (RBDIHS) 76 74 77 80
39: 173 type=169 (RBDIHS) 74 77 80 81
39: 174 type=170 (RBDIHS) 74 77 80 82
39: 175 type=171 (RBDIHS) 78 77 80 82
39: 176 type=171 (RBDIHS) 79 77 80 82
39: 177 type=172 (RBDIHS) 77 80 82 83
39: 178 type=172 (RBDIHS) 77 80 82 86
39: 179 type=173 (RBDIHS) 81 80 82 83
39: 180 type=173 (RBDIHS) 81 80 82 86
39: 181 type=173 (RBDIHS) 80 82 83 84
39: 182 type=173 (RBDIHS) 80 82 83 85
39: 183 type=173 (RBDIHS) 86 82 83 84
39: 184 type=173 (RBDIHS) 86 82 83 85
39: 185 type=173 (RBDIHS) 80 82 86 87
39: 186 type=173 (RBDIHS) 80 82 86 88
39: 187 type=173 (RBDIHS) 83 82 86 87
39: 188 type=173 (RBDIHS) 83 82 86 88
39: 189 type=155 (RBDIHS) 69 89 91 92
39: 190 type=156 (RBDIHS) 69 89 91 93
39: 191 type=155 (RBDIHS) 90 89 91 92
39: 192 type=157 (RBDIHS) 90 89 91 93
39: 193 type=158 (RBDIHS) 89 91 93 95
39: 194 type=159 (RBDIHS) 89 91 93 100
39: 195 type=174 (RBDIHS) 91 93 95 98
39: 196 type=175 (RBDIHS) 100 93 95 98
39: 197 type=147 (RBDIHS) 91 93 95 96
39: 198 type=147 (RBDIHS) 91 93 95 97
39: 199 type=148 (RBDIHS) 94 93 95 96
39: 200 type=148 (RBDIHS) 94 93 95 97
39: 201 type=176 (RBDIHS) 94 93 95 98
39: 202 type=149 (RBDIHS) 100 93 95 96
39: 203 type=149 (RBDIHS) 100 93 95 97
39: 204 type=150 (RBDIHS) 91 93 100 102
39: 205 type=151 (RBDIHS) 95 93 100 102
39: 206 type=177 (RBDIHS) 93 95 98 99
39: 207 type=178 (RBDIHS) 96 95 98 99
39: 208 type=178 (RBDIHS) 97 95 98 99
39: 209 type=155 (RBDIHS) 93 100 102 103
39: 210 type=156 (RBDIHS) 93 100 102 104
39: 211 type=155 (RBDIHS) 101 100 102 103
39: 212 type=157 (RBDIHS) 101 100 102 104
39: 213 type=158 (RBDIHS) 100 102 104 106
39: 214 type=159 (RBDIHS) 100 102 104 115
39: 215 type=179 (RBDIHS) 102 104 106 109
39: 216 type=180 (RBDIHS) 115 104 106 109
39: 217 type=147 (RBDIHS) 102 104 106 107
39: 218 type=147 (RBDIHS) 102 104 106 108
39: 219 type=148 (RBDIHS) 105 104 106 107
39: 220 type=148 (RBDIHS) 105 104 106 108
39: 221 type=148 (RBDIHS) 105 104 106 109
39: 222 type=149 (RBDIHS) 115 104 106 107
39: 223 type=149 (RBDIHS) 115 104 106 108
39: 224 type=150 (RBDIHS) 102 104 115 117
39: 225 type=151 (RBDIHS) 106 104 115 117
39: 226 type=148 (RBDIHS) 104 106 109 110
39: 227 type=148 (RBDIHS) 104 106 109 111
39: 228 type=181 (RBDIHS) 104 106 109 112
39: 229 type=148 (RBDIHS) 107 106 109 110
39: 230 type=148 (RBDIHS) 107 106 109 111
39: 231 type=182 (RBDIHS) 107 106 109 112
39: 232 type=148 (RBDIHS) 108 106 109 110
39: 233 type=148 (RBDIHS) 108 106 109 111
39: 234 type=182 (RBDIHS) 108 106 109 112
39: 235 type=183 (RBDIHS) 106 109 112 113
39: 236 type=183 (RBDIHS) 106 109 112 114
39: 237 type=155 (RBDIHS) 104 115 117 118
39: 238 type=156 (RBDIHS) 104 115 117 119
39: 239 type=155 (RBDIHS) 116 115 117 118
39: 240 type=157 (RBDIHS) 116 115 117 119
39: 241 type=158 (RBDIHS) 115 117 119 121
39: 242 type=159 (RBDIHS) 115 117 119 134
39: 243 type=184 (RBDIHS) 117 119 121 124
39: 244 type=185 (RBDIHS) 134 119 121 124
39: 245 type=147 (RBDIHS) 117 119 121 122
39: 246 type=147 (RBDIHS) 117 119 121 123
39: 247 type=148 (RBDIHS) 120 119 121 122
39: 248 type=148 (RBDIHS) 120 119 121 123
39: 249 type=148 (RBDIHS) 120 119 121 124
39: 250 type=149 (RBDIHS) 134 119 121 122
39: 251 type=149 (RBDIHS) 134 119 121 123
39: 252 type=150 (RBDIHS) 117 119 134 136
39: 253 type=151 (RBDIHS) 121 119 134 136
39: 254 type=148 (RBDIHS) 119 121 124 125
39: 255 type=152 (RBDIHS) 119 121 124 126
39: 256 type=152 (RBDIHS) 119 121 124 130
39: 257 type=148 (RBDIHS) 122 121 124 125
39: 258 type=148 (RBDIHS) 122 121 124 126
39: 259 type=148 (RBDIHS) 122 121 124 130
39: 260 type=148 (RBDIHS) 123 121 124 125
39: 261 type=148 (RBDIHS) 123 121 124 126
39: 262 type=148 (RBDIHS) 123 121 124 130
39: 263 type=148 (RBDIHS) 121 124 126 127
39: 264 type=148 (RBDIHS) 121 124 126 128
39: 265 type=148 (RBDIHS) 121 124 126 129
39: 266 type=148 (RBDIHS) 125 124 126 127
39: 267 type=148 (RBDIHS) 125 124 126 128
39: 268 type=148 (RBDIHS) 125 124 126 129
39: 269 type=148 (RBDIHS) 130 124 126 127
39: 270 type=148 (RBDIHS) 130 124 126 128
39: 271 type=148 (RBDIHS) 130 124 126 129
39: 272 type=148 (RBDIHS) 121 124 130 131
39: 273 type=148 (RBDIHS) 121 124 130 132
39: 274 type=148 (RBDIHS) 121 124 130 133
39: 275 type=148 (RBDIHS) 125 124 130 131
39: 276 type=148 (RBDIHS) 125 124 130 132
39: 277 type=148 (RBDIHS) 125 124 130 133
39: 278 type=148 (RBDIHS) 126 124 130 131
39: 279 type=148 (RBDIHS) 126 124 130 132
39: 280 type=148 (RBDIHS) 126 124 130 133
39: 281 type=155 (RBDIHS) 119 134 136 137
39: 282 type=156 (RBDIHS) 119 134 136 138
39: 283 type=155 (RBDIHS) 135 134 136 137
39: 284 type=157 (RBDIHS) 135 134 136 138
39: 285 type=158 (RBDIHS) 134 136 138 140
39: 286 type=159 (RBDIHS) 134 136 138 144
39: 287 type=147 (RBDIHS) 136 138 140 141
39: 288 type=147 (RBDIHS) 136 138 140 142
39: 289 type=147 (RBDIHS) 136 138 140 143
39: 290 type=148 (RBDIHS) 139 138 140 141
39: 291 type=148 (RBDIHS) 139 138 140 142
39: 292 type=148 (RBDIHS) 139 138 140 143
39: 293 type=149 (RBDIHS) 144 138 140 141
39: 294 type=149 (RBDIHS) 144 138 140 142
39: 295 type=149 (RBDIHS) 144 138 140 143
39: 296 type=150 (RBDIHS) 136 138 144 146
39: 297 type=151 (RBDIHS) 140 138 144 146
39: 298 type=155 (RBDIHS) 138 144 146 147
39: 299 type=156 (RBDIHS) 138 144 146 148
39: 300 type=155 (RBDIHS) 145 144 146 147
39: 301 type=157 (RBDIHS) 145 144 146 148
39: 302 type=158 (RBDIHS) 144 146 148 150
39: 303 type=159 (RBDIHS) 144 146 148 154
39: 304 type=147 (RBDIHS) 146 148 150 151
39: 305 type=147 (RBDIHS) 146 148 150 152
39: 306 type=147 (RBDIHS) 146 148 150 153
39: 307 type=148 (RBDIHS) 149 148 150 151
39: 308 type=148 (RBDIHS) 149 148 150 152
39: 309 type=148 (RBDIHS) 149 148 150 153
39: 310 type=149 (RBDIHS) 154 148 150 151
39: 311 type=149 (RBDIHS) 154 148 150 152
39: 312 type=149 (RBDIHS) 154 148 150 153
39: Restricted Dih.:
39: nr: 0
39: CBT Dih.:
39: nr: 0
39: Fourier Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Tab. Dih.:
39: nr: 0
39: CMAP Dih.:
39: nr: 0
39: GB 1-2 Pol. (unused):
39: nr: 0
39: GB 1-3 Pol. (unused):
39: nr: 0
39: GB 1-4 Pol. (unused):
39: nr: 0
39: GB Polarization (unused):
39: nr: 0
39: Nonpolar Sol. (unused):
39: nr: 0
39: LJ-14:
39: nr: 1197
39: iatoms:
39: 0 type=186 (LJ14) 0 7
39: 1 type=186 (LJ14) 0 8
39: 2 type=187 (LJ14) 0 9
39: 3 type=188 (LJ14) 0 23
39: 4 type=189 (LJ14) 0 24
39: 5 type=190 (LJ14) 1 5
39: 6 type=190 (LJ14) 1 6
39: 7 type=190 (LJ14) 1 22
39: 8 type=190 (LJ14) 2 5
39: 9 type=190 (LJ14) 2 6
39: 10 type=190 (LJ14) 2 22
39: 11 type=190 (LJ14) 3 5
39: 12 type=190 (LJ14) 3 6
39: 13 type=190 (LJ14) 3 22
39: 14 type=191 (LJ14) 4 10
39: 15 type=191 (LJ14) 4 11
39: 16 type=192 (LJ14) 4 12
39: 17 type=190 (LJ14) 4 25
39: 18 type=192 (LJ14) 4 26
39: 19 type=193 (LJ14) 5 7
39: 20 type=193 (LJ14) 5 8
39: 21 type=191 (LJ14) 5 9
39: 22 type=194 (LJ14) 5 23
39: 23 type=186 (LJ14) 5 24
39: 24 type=191 (LJ14) 6 13
39: 25 type=191 (LJ14) 6 14
39: 26 type=192 (LJ14) 6 15
39: 27 type=195 (LJ14) 6 23
39: 28 type=187 (LJ14) 6 24
39: 29 type=193 (LJ14) 7 10
39: 30 type=193 (LJ14) 7 11
39: 31 type=191 (LJ14) 7 12
39: 32 type=196 (LJ14) 7 22
39: 33 type=193 (LJ14) 8 10
39: 34 type=193 (LJ14) 8 11
39: 35 type=191 (LJ14) 8 12
39: 36 type=196 (LJ14) 8 22
39: 37 type=191 (LJ14) 9 16
39: 38 type=191 (LJ14) 9 17
39: 39 type=187 (LJ14) 9 18
39: 40 type=197 (LJ14) 9 22
39: 41 type=193 (LJ14) 10 13
39: 42 type=193 (LJ14) 10 14
39: 43 type=191 (LJ14) 10 15
39: 44 type=193 (LJ14) 11 13
39: 45 type=193 (LJ14) 11 14
39: 46 type=191 (LJ14) 11 15
39: 47 type=190 (LJ14) 12 19
39: 48 type=190 (LJ14) 12 20
39: 49 type=190 (LJ14) 12 21
39: 50 type=193 (LJ14) 13 16
39: 51 type=193 (LJ14) 13 17
39: 52 type=186 (LJ14) 13 18
39: 53 type=193 (LJ14) 14 16
39: 54 type=193 (LJ14) 14 17
39: 55 type=186 (LJ14) 14 18
39: 56 type=190 (LJ14) 16 19
39: 57 type=190 (LJ14) 16 20
39: 58 type=190 (LJ14) 16 21
39: 59 type=190 (LJ14) 17 19
39: 60 type=190 (LJ14) 17 20
39: 61 type=190 (LJ14) 17 21
39: 62 type=196 (LJ14) 22 27
39: 63 type=197 (LJ14) 22 28
39: 64 type=198 (LJ14) 22 38
39: 65 type=190 (LJ14) 23 25
39: 66 type=195 (LJ14) 23 26
39: 67 type=186 (LJ14) 24 29
39: 68 type=187 (LJ14) 24 30
39: 69 type=187 (LJ14) 24 34
39: 70 type=188 (LJ14) 24 39
39: 71 type=189 (LJ14) 24 40
39: 72 type=190 (LJ14) 25 27
39: 73 type=190 (LJ14) 25 28
39: 74 type=190 (LJ14) 25 38
39: 75 type=191 (LJ14) 26 31
39: 76 type=191 (LJ14) 26 32
39: 77 type=191 (LJ14) 26 33
39: 78 type=191 (LJ14) 26 35
39: 79 type=191 (LJ14) 26 36
39: 80 type=191 (LJ14) 26 37
39: 81 type=190 (LJ14) 26 41
39: 82 type=192 (LJ14) 26 42
39: 83 type=193 (LJ14) 27 29
39: 84 type=191 (LJ14) 27 30
39: 85 type=191 (LJ14) 27 34
39: 86 type=194 (LJ14) 27 39
39: 87 type=186 (LJ14) 27 40
39: 88 type=195 (LJ14) 28 39
39: 89 type=187 (LJ14) 28 40
39: 90 type=193 (LJ14) 29 31
39: 91 type=193 (LJ14) 29 32
39: 92 type=193 (LJ14) 29 33
39: 93 type=193 (LJ14) 29 35
39: 94 type=193 (LJ14) 29 36
39: 95 type=193 (LJ14) 29 37
39: 96 type=196 (LJ14) 29 38
39: 97 type=191 (LJ14) 30 35
39: 98 type=191 (LJ14) 30 36
39: 99 type=191 (LJ14) 30 37
39: 100 type=197 (LJ14) 30 38
39: 101 type=191 (LJ14) 31 34
39: 102 type=191 (LJ14) 32 34
39: 103 type=191 (LJ14) 33 34
39: 104 type=197 (LJ14) 34 38
39: 105 type=196 (LJ14) 38 43
39: 106 type=197 (LJ14) 38 44
39: 107 type=198 (LJ14) 38 58
39: 108 type=190 (LJ14) 39 41
39: 109 type=195 (LJ14) 39 42
39: 110 type=186 (LJ14) 40 45
39: 111 type=186 (LJ14) 40 46
39: 112 type=199 (LJ14) 40 47
39: 113 type=188 (LJ14) 40 59
39: 114 type=189 (LJ14) 40 60
39: 115 type=190 (LJ14) 41 43
39: 116 type=190 (LJ14) 41 44
39: 117 type=190 (LJ14) 41 58
39: 118 type=200 (LJ14) 42 48
39: 119 type=200 (LJ14) 42 50
39: 120 type=190 (LJ14) 42 61
39: 121 type=192 (LJ14) 42 62
39: 122 type=193 (LJ14) 43 45
39: 123 type=193 (LJ14) 43 46
39: 124 type=201 (LJ14) 43 47
39: 125 type=194 (LJ14) 43 59
39: 126 type=186 (LJ14) 43 60
39: 127 type=202 (LJ14) 44 49
39: 128 type=202 (LJ14) 44 51
39: 129 type=200 (LJ14) 44 52
39: 130 type=200 (LJ14) 44 54
39: 131 type=195 (LJ14) 44 59
39: 132 type=187 (LJ14) 44 60
39: 133 type=201 (LJ14) 45 48
39: 134 type=201 (LJ14) 45 50
39: 135 type=196 (LJ14) 45 58
39: 136 type=201 (LJ14) 46 48
39: 137 type=201 (LJ14) 46 50
39: 138 type=196 (LJ14) 46 58
39: 139 type=203 (LJ14) 47 53
39: 140 type=203 (LJ14) 47 55
39: 141 type=204 (LJ14) 47 56
39: 142 type=205 (LJ14) 47 58
39: 143 type=203 (LJ14) 48 51
39: 144 type=204 (LJ14) 48 54
39: 145 type=203 (LJ14) 48 57
39: 146 type=203 (LJ14) 49 50
39: 147 type=206 (LJ14) 49 53
39: 148 type=203 (LJ14) 49 56
39: 149 type=204 (LJ14) 50 52
39: 150 type=203 (LJ14) 50 57
39: 151 type=206 (LJ14) 51 55
39: 152 type=203 (LJ14) 51 56
39: 153 type=203 (LJ14) 52 55
39: 154 type=203 (LJ14) 53 54
39: 155 type=206 (LJ14) 53 57
39: 156 type=206 (LJ14) 55 57
39: 157 type=196 (LJ14) 58 63
39: 158 type=196 (LJ14) 58 64
39: 159 type=198 (LJ14) 58 65
39: 160 type=190 (LJ14) 59 61
39: 161 type=195 (LJ14) 59 62
39: 162 type=188 (LJ14) 60 66
39: 163 type=189 (LJ14) 60 67
39: 164 type=190 (LJ14) 61 63
39: 165 type=190 (LJ14) 61 64
39: 166 type=190 (LJ14) 61 65
39: 167 type=190 (LJ14) 62 68
39: 168 type=192 (LJ14) 62 69
39: 169 type=194 (LJ14) 63 66
39: 170 type=186 (LJ14) 63 67
39: 171 type=194 (LJ14) 64 66
39: 172 type=186 (LJ14) 64 67
39: 173 type=196 (LJ14) 65 70
39: 174 type=197 (LJ14) 65 71
39: 175 type=198 (LJ14) 65 89
39: 176 type=190 (LJ14) 66 68
39: 177 type=195 (LJ14) 66 69
39: 178 type=186 (LJ14) 67 72
39: 179 type=186 (LJ14) 67 73
39: 180 type=187 (LJ14) 67 74
39: 181 type=188 (LJ14) 67 90
39: 182 type=189 (LJ14) 67 91
39: 183 type=190 (LJ14) 68 70
39: 184 type=190 (LJ14) 68 71
39: 185 type=190 (LJ14) 68 89
39: 186 type=191 (LJ14) 69 75
39: 187 type=191 (LJ14) 69 76
39: 188 type=192 (LJ14) 69 77
39: 189 type=190 (LJ14) 69 92
39: 190 type=192 (LJ14) 69 93
39: 191 type=193 (LJ14) 70 72
39: 192 type=193 (LJ14) 70 73
39: 193 type=191 (LJ14) 70 74
39: 194 type=194 (LJ14) 70 90
39: 195 type=186 (LJ14) 70 91
39: 196 type=191 (LJ14) 71 78
39: 197 type=191 (LJ14) 71 79
39: 198 type=187 (LJ14) 71 80
39: 199 type=195 (LJ14) 71 90
39: 200 type=187 (LJ14) 71 91
39: 201 type=193 (LJ14) 72 75
39: 202 type=193 (LJ14) 72 76
39: 203 type=191 (LJ14) 72 77
39: 204 type=196 (LJ14) 72 89
39: 205 type=193 (LJ14) 73 75
39: 206 type=193 (LJ14) 73 76
39: 207 type=191 (LJ14) 73 77
39: 208 type=196 (LJ14) 73 89
39: 209 type=190 (LJ14) 74 81
39: 210 type=207 (LJ14) 74 82
39: 211 type=197 (LJ14) 74 89
39: 212 type=193 (LJ14) 75 78
39: 213 type=193 (LJ14) 75 79
39: 214 type=186 (LJ14) 75 80
39: 215 type=193 (LJ14) 76 78
39: 216 type=193 (LJ14) 76 79
39: 217 type=186 (LJ14) 76 80
39: 218 type=187 (LJ14) 77 83
39: 219 type=187 (LJ14) 77 86
39: 220 type=190 (LJ14) 78 81
39: 221 type=208 (LJ14) 78 82
39: 222 type=190 (LJ14) 79 81
39: 223 type=208 (LJ14) 79 82
39: 224 type=190 (LJ14) 80 84
39: 225 type=190 (LJ14) 80 85
39: 226 type=190 (LJ14) 80 87
39: 227 type=190 (LJ14) 80 88
39: 228 type=190 (LJ14) 81 83
39: 229 type=190 (LJ14) 81 86
39: 230 type=190 (LJ14) 83 87
39: 231 type=190 (LJ14) 83 88
39: 232 type=190 (LJ14) 84 86
39: 233 type=190 (LJ14) 85 86
39: 234 type=196 (LJ14) 89 94
39: 235 type=197 (LJ14) 89 95
39: 236 type=198 (LJ14) 89 100
39: 237 type=190 (LJ14) 90 92
39: 238 type=195 (LJ14) 90 93
39: 239 type=186 (LJ14) 91 96
39: 240 type=186 (LJ14) 91 97
39: 241 type=209 (LJ14) 91 98
39: 242 type=188 (LJ14) 91 101
39: 243 type=189 (LJ14) 91 102
39: 244 type=190 (LJ14) 92 94
39: 245 type=190 (LJ14) 92 95
39: 246 type=190 (LJ14) 92 100
39: 247 type=190 (LJ14) 93 99
39: 248 type=190 (LJ14) 93 103
39: 249 type=192 (LJ14) 93 104
39: 250 type=193 (LJ14) 94 96
39: 251 type=193 (LJ14) 94 97
39: 252 type=210 (LJ14) 94 98
39: 253 type=194 (LJ14) 94 101
39: 254 type=186 (LJ14) 94 102
39: 255 type=195 (LJ14) 95 101
39: 256 type=187 (LJ14) 95 102
39: 257 type=190 (LJ14) 96 99
39: 258 type=196 (LJ14) 96 100
39: 259 type=190 (LJ14) 97 99
39: 260 type=196 (LJ14) 97 100
39: 261 type=211 (LJ14) 98 100
39: 262 type=196 (LJ14) 100 105
39: 263 type=197 (LJ14) 100 106
39: 264 type=198 (LJ14) 100 115
39: 265 type=190 (LJ14) 101 103
39: 266 type=195 (LJ14) 101 104
39: 267 type=186 (LJ14) 102 107
39: 268 type=186 (LJ14) 102 108
39: 269 type=187 (LJ14) 102 109
39: 270 type=188 (LJ14) 102 116
39: 271 type=189 (LJ14) 102 117
39: 272 type=190 (LJ14) 103 105
39: 273 type=190 (LJ14) 103 106
39: 274 type=190 (LJ14) 103 115
39: 275 type=191 (LJ14) 104 110
39: 276 type=191 (LJ14) 104 111
39: 277 type=197 (LJ14) 104 112
39: 278 type=190 (LJ14) 104 118
39: 279 type=192 (LJ14) 104 119
39: 280 type=193 (LJ14) 105 107
39: 281 type=193 (LJ14) 105 108
39: 282 type=191 (LJ14) 105 109
39: 283 type=194 (LJ14) 105 116
39: 284 type=186 (LJ14) 105 117
39: 285 type=195 (LJ14) 106 113
39: 286 type=195 (LJ14) 106 114
39: 287 type=195 (LJ14) 106 116
39: 288 type=187 (LJ14) 106 117
39: 289 type=193 (LJ14) 107 110
39: 290 type=193 (LJ14) 107 111
39: 291 type=196 (LJ14) 107 112
39: 292 type=196 (LJ14) 107 115
39: 293 type=193 (LJ14) 108 110
39: 294 type=193 (LJ14) 108 111
39: 295 type=196 (LJ14) 108 112
39: 296 type=196 (LJ14) 108 115
39: 297 type=197 (LJ14) 109 115
39: 298 type=194 (LJ14) 110 113
39: 299 type=194 (LJ14) 110 114
39: 300 type=194 (LJ14) 111 113
39: 301 type=194 (LJ14) 111 114
39: 302 type=196 (LJ14) 115 120
39: 303 type=197 (LJ14) 115 121
39: 304 type=198 (LJ14) 115 134
39: 305 type=190 (LJ14) 116 118
39: 306 type=195 (LJ14) 116 119
39: 307 type=186 (LJ14) 117 122
39: 308 type=186 (LJ14) 117 123
39: 309 type=187 (LJ14) 117 124
39: 310 type=188 (LJ14) 117 135
39: 311 type=189 (LJ14) 117 136
39: 312 type=190 (LJ14) 118 120
39: 313 type=190 (LJ14) 118 121
39: 314 type=190 (LJ14) 118 134
39: 315 type=191 (LJ14) 119 125
39: 316 type=192 (LJ14) 119 126
39: 317 type=192 (LJ14) 119 130
39: 318 type=190 (LJ14) 119 137
39: 319 type=192 (LJ14) 119 138
39: 320 type=193 (LJ14) 120 122
39: 321 type=193 (LJ14) 120 123
39: 322 type=191 (LJ14) 120 124
39: 323 type=194 (LJ14) 120 135
39: 324 type=186 (LJ14) 120 136
39: 325 type=191 (LJ14) 121 127
39: 326 type=191 (LJ14) 121 128
39: 327 type=191 (LJ14) 121 129
39: 328 type=191 (LJ14) 121 131
39: 329 type=191 (LJ14) 121 132
39: 330 type=191 (LJ14) 121 133
39: 331 type=195 (LJ14) 121 135
39: 332 type=187 (LJ14) 121 136
39: 333 type=193 (LJ14) 122 125
39: 334 type=191 (LJ14) 122 126
39: 335 type=191 (LJ14) 122 130
39: 336 type=196 (LJ14) 122 134
39: 337 type=193 (LJ14) 123 125
39: 338 type=191 (LJ14) 123 126
39: 339 type=191 (LJ14) 123 130
39: 340 type=196 (LJ14) 123 134
39: 341 type=197 (LJ14) 124 134
39: 342 type=193 (LJ14) 125 127
39: 343 type=193 (LJ14) 125 128
39: 344 type=193 (LJ14) 125 129
39: 345 type=193 (LJ14) 125 131
39: 346 type=193 (LJ14) 125 132
39: 347 type=193 (LJ14) 125 133
39: 348 type=191 (LJ14) 126 131
39: 349 type=191 (LJ14) 126 132
39: 350 type=191 (LJ14) 126 133
39: 351 type=191 (LJ14) 127 130
39: 352 type=191 (LJ14) 128 130
39: 353 type=191 (LJ14) 129 130
39: 354 type=196 (LJ14) 134 139
39: 355 type=197 (LJ14) 134 140
39: 356 type=198 (LJ14) 134 144
39: 357 type=190 (LJ14) 135 137
39: 358 type=195 (LJ14) 135 138
39: 359 type=186 (LJ14) 136 141
39: 360 type=186 (LJ14) 136 142
39: 361 type=186 (LJ14) 136 143
39: 362 type=188 (LJ14) 136 145
39: 363 type=189 (LJ14) 136 146
39: 364 type=190 (LJ14) 137 139
39: 365 type=190 (LJ14) 137 140
39: 366 type=190 (LJ14) 137 144
39: 367 type=190 (LJ14) 138 147
39: 368 type=192 (LJ14) 138 148
39: 369 type=193 (LJ14) 139 141
39: 370 type=193 (LJ14) 139 142
39: 371 type=193 (LJ14) 139 143
39: 372 type=194 (LJ14) 139 145
39: 373 type=186 (LJ14) 139 146
39: 374 type=195 (LJ14) 140 145
39: 375 type=187 (LJ14) 140 146
39: 376 type=196 (LJ14) 141 144
39: 377 type=196 (LJ14) 142 144
39: 378 type=196 (LJ14) 143 144
39: 379 type=196 (LJ14) 144 149
39: 380 type=197 (LJ14) 144 150
39: 381 type=198 (LJ14) 144 154
39: 382 type=190 (LJ14) 145 147
39: 383 type=195 (LJ14) 145 148
39: 384 type=186 (LJ14) 146 151
39: 385 type=186 (LJ14) 146 152
39: 386 type=186 (LJ14) 146 153
39: 387 type=188 (LJ14) 146 155
39: 388 type=190 (LJ14) 147 149
39: 389 type=190 (LJ14) 147 150
39: 390 type=190 (LJ14) 147 154
39: 391 type=193 (LJ14) 149 151
39: 392 type=193 (LJ14) 149 152
39: 393 type=193 (LJ14) 149 153
39: 394 type=194 (LJ14) 149 155
39: 395 type=195 (LJ14) 150 155
39: 396 type=196 (LJ14) 151 154
39: 397 type=196 (LJ14) 152 154
39: 398 type=196 (LJ14) 153 154
39: Coulomb-14:
39: nr: 0
39: LJC-14 q:
39: nr: 0
39: LJC Pairs NB:
39: nr: 0
39: LJ (SR):
39: nr: 0
39: Buck.ham (SR):
39: nr: 0
39: LJ (unused):
39: nr: 0
39: B.ham (unused):
39: nr: 0
39: Disper. corr.:
39: nr: 0
39: Coulomb (SR):
39: nr: 0
39: Coul (unused):
39: nr: 0
39: RF excl.:
39: nr: 0
39: Coul. recip.:
39: nr: 0
39: LJ recip.:
39: nr: 0
39: DPD:
39: nr: 0
39: Polarization:
39: nr: 0
39: Water Pol.:
39: nr: 0
39: Thole Pol.:
39: nr: 0
39: Anharm. Pol.:
39: nr: 0
39: Position Rest.:
39: nr: 0
39: Flat-bottom posres:
39: nr: 0
39: Dis. Rest.:
39: nr: 0
39: D.R.Viol. (nm):
39: nr: 0
39: Orient. Rest.:
39: nr: 0
39: Ori. R. RMSD:
39: nr: 0
39: Angle Rest.:
39: nr: 0
39: Angle Rest. Z:
39: nr: 0
39: Dih. Rest.:
39: nr: 0
39: Dih. Rest. Viol.:
39: nr: 0
39: Constraint:
39: nr: 0
39: Constr. No Conn.:
39: nr: 0
39: Settle:
39: nr: 0
39: Virtual site 2:
39: nr: 0
39: Virtual site 2fd:
39: nr: 0
39: Virtual site 3:
39: nr: 0
39: Virtual site 3fd:
39: nr: 0
39: Virtual site 3fad:
39: nr: 0
39: Virtual site 3out:
39: nr: 0
39: Virtual site 4fd:
39: nr: 0
39: Virtual site 4fdn:
39: nr: 0
39: Virtual site N:
39: nr: 0
39: COM Pull En.:
39: nr: 0
39: Density fitting:
39: nr: 0
39: Quantum En.:
39: nr: 0
39: Potential:
39: nr: 0
39: Kinetic En.:
39: nr: 0
39: Total Energy:
39: nr: 0
39: Conserved En.:
39: nr: 0
39: Temperature:
39: nr: 0
39: Vir. Temp. (not used):
39: nr: 0
39: Pres. DC:
39: nr: 0
39: Pressure:
39: nr: 0
39: dH/dl constr.:
39: nr: 0
39: dVremain/dl:
39: nr: 0
39: dEkin/dl:
39: nr: 0
39: dVcoul/dl:
39: nr: 0
39: dVvdw/dl:
39: nr: 0
39: dVbonded/dl:
39: nr: 0
39: dVrestraint/dl:
39: nr: 0
39: dVtemperature/dl:
39: nr: 0
39: grp[T-Coupling ] nr=1, name=[ rest]
39: grp[Energy Mon. ] nr=1, name=[ rest]
39: grp[Acceleration] nr=1, name=[ rest]
39: grp[Freeze ] nr=1, name=[ rest]
39: grp[User1 ] nr=1, name=[ rest]
39: grp[User2 ] nr=1, name=[ rest]
39: grp[VCM ] nr=1, name=[ rest]
39: grp[Compressed X] nr=1, name=[ rest]
39: grp[Or. Res. Fit] nr=1, name=[ rest]
39: grp[QMMM ] nr=1, name=[ rest]
39: grpname (11):
39: grpname[0]={name="System"}
39: grpname[1]={name="Protein"}
39: grpname[2]={name="Protein-H"}
39: grpname[3]={name="C-alpha"}
39: grpname[4]={name="Backbone"}
39: grpname[5]={name="MainChain"}
39: grpname[6]={name="MainChain+Cb"}
39: grpname[7]={name="MainChain+H"}
39: grpname[8]={name="SideChain"}
39: grpname[9]={name="SideChain-H"}
39: grpname[10]={name="rest"}
39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
39: allocated 0 0 0 0 0 0 0 0 0 0
39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
39: box (3x3):
39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
39: box_rel (3x3):
39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv (3x3):
39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev (3x3):
39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev (3x3):
39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev (3x3):
39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: nosehoover_xi: not available
39: x (156x3):
39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
39: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
39: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
39: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
39: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
39: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
39: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
39: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
39: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
39: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
39: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
39: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
39: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
39: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
39: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
39: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
39: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
39: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
39: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
39: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
39: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
39: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
39: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
39: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
39: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
39: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
39: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
39: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
39: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
39: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
39: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
39: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
39: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
39: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
39: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
39: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
39: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
39: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
39: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
39: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
39: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
39: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
39: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
39: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
39: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
39: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
39: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
39: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
39: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
39: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
39: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
39: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
39: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
39: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
39: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
39: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
39: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
39: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
39: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
39: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
39: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
39: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
39: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
39: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
39: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
39: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
39: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
39: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
39: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
39: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
39: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
39: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
39: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
39: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
39: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
39: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
39: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
39: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
39: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
39: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
39: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
39: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
39: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
39: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
39: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
39: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
39: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
39: v (156x3):
39: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: Group statistics
39: T-Coupling : 156 (total 156 atoms)
39: Energy Mon. : 156 (total 156 atoms)
39: Acceleration: 156 (total 156 atoms)
39: Freeze : 156 (total 156 atoms)
39: User1 : 156 (total 156 atoms)
39: User2 : 156 (total 156 atoms)
39: VCM : 156 (total 156 atoms)
39: Compressed X: 156 (total 156 atoms)
39: Or. Res. Fit: 156 (total 156 atoms)
39: QMMM : 156 (total 156 atoms)
39: [ OK ] DumpTest.WorksWithTpr (75 ms)
39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (2 ms)
39: [----------] 2 tests from DumpTest (77 ms total)
39:
39: [----------] 4 tests from ReportMethodsTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -673202485
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectInformation
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
39: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms)
39: [ RUN ] ReportMethodsTest.ToolEndToEndTest
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
39: section: Methods
39: subsection: Simulation system
39: A system of 1 molecules (156 atoms) was simulated.
39:
39: subsection: Simulation settings
39: A total of 0 ns were simulated with a time step of 1 fs.
39: Neighbor searching was performed every 10 steps.
39: The Cut-off algorithm was used for electrostatic interactions.
39: with a cut-off of 1 nm.
39: A single cut-off of 1.1 nm was used for Van der Waals interactions.
39: [ OK ] ReportMethodsTest.ToolEndToEndTest (2 ms)
39: [----------] 4 tests from ReportMethodsTest (3 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: trr version: GMX_trn_file (single precision)
39:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (6 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (8 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (5 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (34 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (1 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (14 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 18 tests from 4 test cases ran. (2059 ms total)
39: [ PASSED ] 18 tests.
39/54 Test #39: ToolUnitTests ....................... Passed 2.08 sec
test 40
Start 40: FileIOTests
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 33 tests from 8 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from FileMD5Test
40: [ RUN ] FileMD5Test.CanComputeMD5
40: [ OK ] FileMD5Test.CanComputeMD5 (1 ms)
40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms)
40: [----------] 2 tests from FileMD5Test (1 ms total)
40:
40: [----------] 3 tests from MrcSerializer
40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (5 ms)
40: [----------] 3 tests from MrcSerializer (5 ms total)
40:
40: [----------] 4 tests from MrcDensityMap
40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (6 ms)
40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms)
40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms)
40: [----------] 4 tests from MrcDensityMap (9 ms total)
40:
40: [----------] 8 tests from MrcDensityMapHeaderTest
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.IsSane
40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
40: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total)
40:
40: [----------] 9 tests from ReadTest
40: [ RUN ] ReadTest.get_eint_ReadsInteger
40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutString (1 ms)
40: [ RUN ] ReadTest.get_eint64_ReadsInteger
40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsInteger
40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsFloat
40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
40: [ RUN ] ReadTest.get_ereal_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not a
40: real value
40:
40:
40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
40: [----------] 9 tests from ReadTest (1 ms total)
40:
40: [----------] 1 test from FileIOXdrSerializerTest
40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms)
40: [----------] 1 test from FileIOXdrSerializerTest (0 ms total)
40:
40: [----------] 2 tests from TngTest
40: [ RUN ] TngTest.CanOpenTngFile
40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
40: [ OK ] TngTest.CanOpenTngFile (0 ms)
40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
40: [----------] 2 tests from TngTest (0 ms total)
40:
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (4 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms)
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (8 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 33 tests from 8 test cases ran. (26 ms total)
40: [ PASSED ] 33 tests.
40/54 Test #40: FileIOTests ......................... Passed 0.05 sec
test 41
Start 41: SelectionUnitTests
41: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 192 tests from 11 test cases.
41: [----------] Global test environment set-up.
41: [----------] 1 test from IndexGroupTest
41: [ RUN ] IndexGroupTest.RemovesDuplicates
41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
41: [----------] 1 test from IndexGroupTest (0 ms total)
41:
41: [----------] 15 tests from IndexBlockTest
41: [ RUN ] IndexBlockTest.CreatesUnknownBlock
41: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms)
41: [ RUN ] IndexBlockTest.CreatesAtomBlock
41: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesSingleBlock
41: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
41: [----------] 15 tests from IndexBlockTest (4 ms total)
41:
41: [----------] 11 tests from IndexMapTest
41: [ RUN ] IndexMapTest.InitializesAtomBlock
41: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
41: [ RUN ] IndexMapTest.InitializesMoleculeBlock
41: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
41: [ RUN ] IndexMapTest.MapsSingleBlock
41: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocks
41: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms)
41: [ RUN ] IndexMapTest.HandlesMultipleRequests
41: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms)
41: [----------] 11 tests from IndexMapTest (5 ms total)
41:
41: [----------] 3 tests from IndexGroupsAndNamesTest
41: [ RUN ] IndexGroupsAndNamesTest.containsNames
41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms)
41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
41: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
41:
41: [----------] 15 tests from NeighborhoodSearchTest
41: [ RUN ] NeighborhoodSearchTest.SimpleSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSearch (35 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (32 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchBox
41: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (24 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (9 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (5 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (5 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (96 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (8 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (2 ms)
41: [----------] 15 tests from NeighborhoodSearchTest (221 ms total)
41:
41: [----------] 12 tests from PositionCalculationTest
41: [ RUN ] PositionCalculationTest.ComputesAtomPositions
41: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionMask
41: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms)
41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
41: [----------] 12 tests from PositionCalculationTest (7 ms total)
41:
41: [----------] 29 tests from SelectionCollectionTest
41: [ RUN ] SelectionCollectionTest.HandlesNoSelections
41: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms)
41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (3 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
41: [----------] 29 tests from SelectionCollectionTest (37 ms total)
41:
41: [----------] 14 tests from SelectionCollectionInteractiveTest
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
41: [----------] 14 tests from SelectionCollectionInteractiveTest (24 ms total)
41:
41: [----------] 66 tests from SelectionCollectionDataTest
41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResnr
41: [ OK ] SelectionCollectionDataTest.HandlesResnr (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesChain
41: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMass
41: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCharge
41: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBeta
41: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResname
41: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (17 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (12 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (14 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (6 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (12 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (5 ms)
41: [----------] 66 tests from SelectionCollectionDataTest (327 ms total)
41:
41: [----------] 17 tests from SelectionOptionTest
41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptySelections
41: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelections
41: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesAdjuster
41: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms)
41: [----------] 17 tests from SelectionOptionTest (15 ms total)
41:
41: [----------] 9 tests from SelectionFileOptionTest
41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
41: [----------] 9 tests from SelectionFileOptionTest (8 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 192 tests from 11 test cases ran. (649 ms total)
41: [ PASSED ] 192 tests.
41/54 Test #41: SelectionUnitTests .................. Passed 0.68 sec
test 42
Start 42: MdrunOutputTests
42: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunOutputTests.xml"
42: Test timeout computed to be: 600
42: [==========] Running 12 tests from 5 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from MdrunTest
42: [ RUN ] MdrunTest.WritesHelp
42: [ OK ] MdrunTest.WritesHelp (5 ms)
42: [----------] 1 test from MdrunTest (5 ms total)
42:
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
42: Setting the LD random seed to -102860305
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.257 0.129 199.6
42: (ns/day) (hour/ns)
42: Performance: 1.342 17.878
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (172 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
42: Setting the LD random seed to -1073816201
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.205 0.103 199.4
42: (ns/day) (hour/ns)
42: Performance: 1.680 14.288
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (124 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
42: Setting the LD random seed to -176235163
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.222 0.112 199.4
42: (ns/day) (hour/ns)
42: Performance: 1.549 15.489
42:
Reading frame 0 time 0.000
42: # Atoms 3
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (133 ms)
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (430 ms total)
42:
42: [----------] 2 tests from Argon12/OutputFiles
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.503 0.252 199.8
42: (ns/day) (hour/ns)
42: Performance: 5.834 4.114
42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (274 ms)
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.241 0.121 199.6
42: (ns/day) (hour/ns)
42: Performance: 12.149 1.975
42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (142 ms)
42: [----------] 2 tests from Argon12/OutputFiles (416 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/Trajectories
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
42: Setting the LD random seed to -237118981
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.150 0.075 199.1
42: (ns/day) (hour/ns)
42: Performance: 8.019 2.993
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (101 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
42: Setting the LD random seed to -1597701
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.166 0.083 199.2
42: (ns/day) (hour/ns)
42: Performance: 7.259 3.306
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (108 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
42: Setting the LD random seed to -304087776
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.183 0.092 199.3
42: (ns/day) (hour/ns)
42: Performance: 6.570 3.653
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (117 ms)
42: [----------] 3 tests from MdrunCanWrite/Trajectories (326 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
42: Setting the LD random seed to 1610463223
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.218 0.109 199.3
42: (ns/day) (hour/ns)
42: Performance: 2.368 10.135
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (133 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
42: Setting the LD random seed to 918484700
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.169 0.085 199.2
42: (ns/day) (hour/ns)
42: Performance: 3.062 7.838
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (108 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
42: Setting the LD random seed to -1100497666
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.184 0.093 199.2
42: (ns/day) (hour/ns)
42: Performance: 2.801 8.567
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (117 ms)
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (358 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 12 tests from 5 test cases ran. (1535 ms total)
42: [ PASSED ] 12 tests.
42/54 Test #42: MdrunOutputTests .................... Passed 1.56 sec
test 43
Start 43: MdrunModulesTests
43: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunModulesTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 10 tests from 3 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to -8716297
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.8565400e+03
43: Maximum force = 2.8846870e+03 on atom 3
43: Norm of force = 1.0754448e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (45 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to -8863765
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.7138666e+04
43: Maximum force = 4.3409717e+03 on atom 2
43: Norm of force = 1.2549793e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (25 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (18 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to 761257983
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.214 0.107 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.416 9.933
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.197 0.099 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.366 5.497
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (238 ms)
43: [----------] 4 tests from DensityFittingTest (326 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -151388481
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 174.1
43: (ns/day) (hour/ns)
43: Performance: 98.235 0.244
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (22 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 931077630
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.001 0.001 173.7
43: (ns/day) (hour/ns)
43: Performance: 100.496 0.239
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (23 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 939490803
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.001 0.001 174.7
43: (ns/day) (hour/ns)
43: Performance: 102.052 0.235
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (21 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1445005753
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 182.9
43: (ns/day) (hour/ns)
43: Performance: 65.072 0.369
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (68 ms)
43: [----------] 4 tests from MimicTest (134 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to 1332739711
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 37683.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.241 0.121 199.4
43: (ns/day) (hour/ns)
43: Performance: 4.286 5.599
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (556 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to -120096867
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 43211.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.1977063e+03
43: Maximum force = 1.7794877e+04 on atom 9
43: Norm of force = 7.8732901e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (434 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (991 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 10 tests from 3 test cases ran. (1451 ms total)
43: [ PASSED ] 10 tests.
43/54 Test #43: MdrunModulesTests ................... Passed 1.47 sec
test 44
Start 44: MdrunIOTests
44: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunIOTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 51 tests from 9 test cases.
44: [----------] Global test environment set-up.
44: [----------] 3 tests from GromppTest
44: [ RUN ] GromppTest.EmptyMdpFileWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -17862701
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.EmptyMdpFileWorks (10 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -536872282
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group rest: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorks (9 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -1083515523
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group Methanol: Single, 3 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 3.0 280.0
44: 6.0- 270.0
44: Simulated annealing for group SOL: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group Methanol is 7.20
44: Number of degrees of freedom in T-Coupling group SOL is 4.80
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (10 ms)
44: [----------] 3 tests from GromppTest (29 ms total)
44:
44: [----------] 6 tests from MdrunTerminationTest
44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
44: Setting the LD random seed to -1184924941
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.273 0.137 199.5
44: (ns/day) (hour/ns)
44: Performance: 1.891 12.691
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.146 0.073 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.543 6.774
44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (263 ms)
44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
44: Setting the LD random seed to -340821019
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 1, rlist from 1.024 to 1
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 100 steps, 0.1 ps.
44:
44: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.168 0.084 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.075 7.806
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Setting nsteps to 102
44: Writing statusfile with starting step 0 and length 102 steps...
44: time 0.000 and length 0.102 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.180 0.090 199.4
44: (ns/day) (hour/ns)
44: Performance: 96.906 0.248
44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (208 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
44: Setting the LD random seed to 1172952927
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.152 0.076 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.391 7.077
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.145 0.073 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.566 6.730
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Setting nsteps to 6
44: Writing statusfile with starting step 0 and length 6 steps...
44: time 0.000 and length 0.006 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.156 0.078 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.311 7.249
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Setting nsteps to 8
44: Writing statusfile with starting step 0 and length 8 steps...
44: time 0.000 and length 0.008 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.146 0.073 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.548 6.764
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.001 0.001 157.2
44: (ns/day) (hour/ns)
44: Performance: 122.802 0.195
44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (368 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
44: Setting the LD random seed to -555368965
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.167 0.084 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.094 7.758
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.146 0.074 199.2
44: (ns/day) (hour/ns)
44: Performance: 5.877 4.084
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (190 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
44: Setting the LD random seed to -268765703
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.153 0.077 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.369 7.125
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (102 ms)
44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
44: Setting the LD random seed to -346357801
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.150 0.075 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.447 6.963
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.145 0.073 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.559 6.743
44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (180 ms)
44: [----------] 6 tests from MdrunTerminationTest (1311 ms total)
44:
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.216 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 13.566 1.769
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.713 3.112
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.199 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.800 3.077
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (364 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.224 0.112 199.6
44: (ns/day) (hour/ns)
44: Performance: 13.077 1.835
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.672 3.128
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.6
44: (ns/day) (hour/ns)
44: Performance: 8.459 2.837
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (358 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.222 0.111 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.202 1.818
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.218 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.128 3.367
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.203 3.332
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (383 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.374 0.187 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.851 3.057
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.199 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.792 3.080
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.205 3.331
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (450 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.253 0.127 199.5
44: (ns/day) (hour/ns)
44: Performance: 11.606 2.068
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.250 0.126 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.192 3.876
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.199 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.810 3.073
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (408 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.205 0.103 199.6
44: (ns/day) (hour/ns)
44: Performance: 14.278 1.681
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.692 3.120
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.159 3.352
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (367 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.504 1.655
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.216 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.174 3.345
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.239 3.315
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (375 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.236 0.118 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.419 1.933
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.762 3.092
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.539 2.811
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (367 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.254 0.127 199.4
44: (ns/day) (hour/ns)
44: Performance: 11.535 2.081
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.213 0.107 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.271 3.301
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.245 0.123 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.319 3.798
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (510 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.220 0.110 199.3
44: (ns/day) (hour/ns)
44: Performance: 13.331 1.800
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.242 3.314
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.194 0.098 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.969 3.011
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (466 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.288 0.144 199.4
44: (ns/day) (hour/ns)
44: Performance: 10.180 2.358
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.2
44: (ns/day) (hour/ns)
44: Performance: 6.712 3.576
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.212 0.106 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.311 3.283
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (592 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.221 0.111 199.3
44: (ns/day) (hour/ns)
44: Performance: 13.236 1.813
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.245 3.313
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.195 0.098 199.1
44: (ns/day) (hour/ns)
44: Performance: 7.926 3.028
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (517 ms)
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (5157 ms total)
44:
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.271 0.136 199.3
44: (ns/day) (hour/ns)
44: Performance: 10.800 2.222
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.262 0.132 199.1
44: (ns/day) (hour/ns)
44: Performance: 5.907 4.063
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.276 0.138 199.3
44: (ns/day) (hour/ns)
44: Performance: 5.615 4.274
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (558 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.665 0.333 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.414 5.437
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.265 0.133 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.867 4.091
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.277 0.139 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.593 4.291
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (759 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.260 0.130 199.3
44: (ns/day) (hour/ns)
44: Performance: 11.274 2.129
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.253 0.127 199.1
44: (ns/day) (hour/ns)
44: Performance: 6.129 3.916
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.249 0.125 199.3
44: (ns/day) (hour/ns)
44: Performance: 6.222 3.857
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (624 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.286 0.143 199.4
44: (ns/day) (hour/ns)
44: Performance: 10.244 2.343
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.259 0.130 199.2
44: (ns/day) (hour/ns)
44: Performance: 5.977 4.015
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.255 0.128 199.3
44: (ns/day) (hour/ns)
44: Performance: 6.066 3.957
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (608 ms)
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2550 ms total)
44:
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.549 1.913
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.142 3.360
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.820 3.069
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (381 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.223 0.112 199.5
44: (ns/day) (hour/ns)
44: Performance: 13.161 1.824
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.425 2.849
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.210 3.329
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (366 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.189 0.095 199.4
44: (ns/day) (hour/ns)
44: Performance: 15.504 1.548
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.725 3.107
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.199 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.803 3.076
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (350 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.206 0.103 199.5
44: (ns/day) (hour/ns)
44: Performance: 14.217 1.688
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.145 3.359
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.831 3.065
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (367 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.224 0.112 199.6
44: (ns/day) (hour/ns)
44: Performance: 13.076 1.835
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.687 3.122
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.771 3.088
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (367 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.222 0.111 199.5
44: (ns/day) (hour/ns)
44: Performance: 13.188 1.820
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.422 2.850
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.230 3.320
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (366 ms)
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (2197 ms total)
44:
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.206 0.103 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.248 1.684
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.727 3.106
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.182 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.536 2.812
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (351 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.171 0.086 199.3
44: (ns/day) (hour/ns)
44: Performance: 17.129 1.401
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.143 3.360
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.222 3.323
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (358 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.220 0.110 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.314 1.803
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.629 3.621
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.831 3.065
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (382 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.207 0.104 199.6
44: (ns/day) (hour/ns)
44: Performance: 14.173 1.693
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.219 0.110 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.097 3.382
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.5
44: (ns/day) (hour/ns)
44: Performance: 8.473 2.833
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (359 ms)
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (1451 ms total)
44:
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.219 0.110 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.356 1.797
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.138 3.362
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.830 3.065
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (375 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.204 0.102 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.381 1.669
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.731 3.104
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.197 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.878 3.046
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (358 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.102 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.428 1.663
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.445 2.842
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.223 3.323
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (358 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.204 0.102 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.388 1.668
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.740 3.101
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.226 3.321
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (367 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.253 0.127 199.5
44: (ns/day) (hour/ns)
44: Performance: 11.581 2.072
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.250 0.126 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.191 3.877
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.232 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.697 3.584
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (425 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.237 0.119 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.347 1.944
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.139 3.362
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.229 3.320
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (392 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.102 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.394 1.667
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.436 2.845
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.844 3.060
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (349 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.220 0.110 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.314 1.803
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.639 3.615
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.845 3.059
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (383 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.273 0.137 199.7
44: (ns/day) (hour/ns)
44: Performance: 10.749 2.233
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.219 0.110 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.099 3.381
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.216 0.108 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.177 3.344
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (408 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms)
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (3417 ms total)
44:
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.505 1.655
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.433 2.846
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.255 3.308
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (357 ms)
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (357 ms total)
44:
44: [----------] 3 tests from Checking/InitialConstraintsTest
44: [ RUN ] Checking/InitialConstraintsTest.Works/0
44: Setting the LD random seed to -39
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.175 0.088 199.3
44: (ns/day) (hour/ns)
44: Performance: 1.965 12.215
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (111 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/1
44: Setting the LD random seed to -536904545
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.171 0.086 199.4
44: (ns/day) (hour/ns)
44: Performance: 2.010 11.938
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (108 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: Integrator method md-vv-avek is implemented primarily for validation
44: purposes; for molecular dynamics, you should probably be using md or md-vv
44:
44: Setting the LD random seed to -915425379
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.136 0.068 199.0
44: (ns/day) (hour/ns)
44: Performance: 2.531 9.482
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (92 ms)
44: [----------] 3 tests from Checking/InitialConstraintsTest (311 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 51 tests from 9 test cases ran. (16781 ms total)
44: [ PASSED ] 51 tests.
44/54 Test #44: MdrunIOTests ........................ Passed 16.81 sec
test 45
Start 45: MdrunTests
45: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 12 tests from 5 test cases.
45: [----------] Global test environment set-up.
45: [----------] 1 test from DispersionCorrectionTest
45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 2142762813
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
45: Cleaning up constraints and constant bonded interactions with virtual sites
45: Converted 3 Bonds with virtual sites to connections, 7 left
45: Removed 18 Angles with virtual sites, 21 left
45: Removed 10 Proper Dih.s with virtual sites, 44 left
45: Converted 12 Constraints with virtual sites to connections, 0 left
45: Number of degrees of freedom in T-Coupling group System is 30.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: There are 9 non-linear virtual site constructions. Their contribution to
45: the energy error is approximated. In most cases this does not affect the
45: error significantly.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Changing nstlist from 10 to 50, rlist from 1.016 to 1.167
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Alanine dipeptide in vacuo'
45: 200 steps, 0.4 ps.
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.303 0.152 199.4
45: (ns/day) (hour/ns)
45: Performance: 228.821 0.105
45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (235 ms)
45: [----------] 1 test from DispersionCorrectionTest (235 ms total)
45:
45: [----------] 1 test from OriresTest
45: [ RUN ] OriresTest.OriresCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 1672347519
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 518.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
45: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
45:
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
45: 10 steps, 0.0 ps.
45: turning H bonds into constraints...
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.188 0.094 199.2
45: (ns/day) (hour/ns)
45: Performance: 20.137 1.192
45: [ OK ] OriresTest.OriresCanRun (768 ms)
45: [----------] 1 test from OriresTest (768 ms total)
45:
45: [----------] 3 tests from PmeTest
45: [ RUN ] PmeTest.ReproducesEnergies
45: Setting the LD random seed to 1807678973
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.307 0.154 199.6
45: (ns/day) (hour/ns)
45: Performance: 11.801 2.034
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.221 0.111 199.5
45: (ns/day) (hour/ns)
45: Performance: 16.365 1.467
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45:
45: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.288 0.144 199.6
45: (ns/day) (hour/ns)
45: Performance: 12.588 1.907
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10603 ms)
45: [ RUN ] PmeTest.ScalesTheBox
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1916862764
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.004 0.002 173.6
45: (ns/day) (hour/ns)
45: Performance: 36.948 0.650
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBox (35 ms)
45: [ RUN ] PmeTest.ScalesTheBoxWithWalls
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1675351709
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Searching the wall atom type(s)
45: Number of degrees of freedom in T-Coupling group rest is 13.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: NVE simulation: will use the initial temperature of 966.268 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.013 0.007 188.8
45: (ns/day) (hour/ns)
45: Performance: 12.248 1.960
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBoxWithWalls (30695 ms)
45: [----------] 3 tests from PmeTest (41333 ms total)
45:
45: [----------] 1 test from CompelTest
45: [ RUN ] CompelTest.SwapCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 1604294143
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 1 bonded neighbours molecule type 'NA'
45: Excluding 1 bonded neighbours molecule type 'CL'
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Split0 group 'Ch0' contains 83 atoms.
45: Split1 group 'Ch1' contains 83 atoms.
45: Solvent group 'SOL' contains 11931 atoms.
45: Swap group 'NA+' contains 19 atoms.
45: Swap group 'CL-' contains 19 atoms.
45: Number of degrees of freedom in T-Coupling group System is 27869.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: Removing center of mass motion in the presence of position restraints
45: might cause artifacts. When you are using position restraints to
45: equilibrate a macro-molecule, the artifacts are usually negligible.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Determining initial numbers of ions per compartment.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 2 steps, 0.0 ps.
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 1 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 2.413 1.207 199.9
45: (ns/day) (hour/ns)
45: Performance: 1.074 22.353
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Copying channel fluxes from checkpoint file data
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 2.130 1.065 199.9
45: (ns/day) (hour/ns)
45: Performance: 1.216 19.730
45: [ OK ] CompelTest.SwapCanRun (5365 ms)
45: [----------] 1 test from CompelTest (5365 ms total)
45:
45: [----------] 6 tests from BondedInteractionsTest
45: [ RUN ] BondedInteractionsTest.NormalBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1738374974
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 177.8
45: (ns/day) (hour/ns)
45: Performance: 89.523 0.268
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalBondWorks (22 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1143473369
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 176.2
45: (ns/day) (hour/ns)
45: Performance: 100.357 0.239
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (26 ms)
45: [ RUN ] BondedInteractionsTest.NormalAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 2138037743
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 176.9
45: (ns/day) (hour/ns)
45: Performance: 97.129 0.247
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalAngleWorks (22 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -571482631
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 176.4
45: (ns/day) (hour/ns)
45: Performance: 100.190 0.240
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (24 ms)
45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 2145778687
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 176.0
45: (ns/day) (hour/ns)
45: Performance: 99.859 0.240
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (21 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -541078450
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 176.0
45: (ns/day) (hour/ns)
45: Performance: 100.775 0.238
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (27 ms)
45: [----------] 6 tests from BondedInteractionsTest (142 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 12 tests from 5 test cases ran. (47843 ms total)
45: [ PASSED ] 12 tests.
45:
45: YOU HAVE 12 DISABLED TESTS
45:
45/54 Test #45: MdrunTests .......................... Passed 47.87 sec
test 46
Start 46: MdrunNonIntegratorTests
46: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 58 tests from 5 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from NonbondedBenchTest
46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
46: System size: 3000 atoms
46: Cut-off radius: 1 nm
46: Number of threads: 1
46: Number of iterations: 1
46: Compute energies: no
46: Ewald excl. corr.: analytical
46:
46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
46: total useful
46: Ewald all geom. no 0.000 0.0000 inf inf
46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (214 ms)
46: [----------] 1 test from NonbondedBenchTest (215 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.7990990e+01
46: Maximum force = 1.8629828e+02 on atom 13
46: Norm of force = 8.7721844e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (902 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.5862099e+01
46: Maximum force = 4.2728845e+02 on atom 13
46: Norm of force = 1.8453478e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2334 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1937714e+02
46: Maximum force = 9.9988643e+03 on atom 9
46: Norm of force = 4.6166996e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (434 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5174377e+02
46: Maximum force = 7.4208838e+03 on atom 9
46: Norm of force = 3.5693005e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (441 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.5698413e+02
46: Maximum force = 4.5704984e+02 on atom 17
46: Norm of force = 1.8327747e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (69 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06801e+03 on atom 28
46: F-Norm = 4.26916e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.6941180e+02
46: Maximum force = 2.1832491e+02 on atom 17
46: Norm of force = 7.9220732e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (70 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4250 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.7425699e-01
46: Maximum force = 4.0132303e+00 on atom 1
46: Norm of force = 1.6383944e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.9064207e-01
46: Maximum force = 2.5781622e+00 on atom 1
46: Norm of force = 1.0525302e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.9064207e-01
46: Maximum force = 2.5781622e+00 on atom 1
46: Norm of force = 1.0525302e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1939697e+02
46: Maximum force = 9.9704248e+03 on atom 9
46: Norm of force = 4.6227540e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (439 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5625757e+02
46: Maximum force = 7.5018242e+03 on atom 9
46: Norm of force = 3.6139019e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (437 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 5.6111725e+02
46: Maximum force = 1.2685491e+04 on atom 10
46: Norm of force = 6.0643622e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (437 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1383 ms total)
46:
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.314 0.157 199.7
46: (ns/day) (hour/ns)
46: Performance: 9.345 2.568
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
46:
46: trr version: GMX_trn_file (single precision)
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.008 0.004 194.4
46: (ns/day) (hour/ns)
46: Performance: 346.763 0.069
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (197 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.238 0.119 199.7
46: (ns/day) (hour/ns)
46: Performance: 12.320 1.948
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.008 0.004 194.3
46: (ns/day) (hour/ns)
46: Performance: 346.607 0.069
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (158 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.236 0.118 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.424 1.932
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.008 0.004 194.4
46: (ns/day) (hour/ns)
46: Performance: 349.319 0.069
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (158 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.220 0.110 199.5
46: (ns/day) (hour/ns)
46: Performance: 13.330 1.800
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.008 0.004 194.4
46: (ns/day) (hour/ns)
46: Performance: 349.379 0.069
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (150 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.358 0.180 199.7
46: (ns/day) (hour/ns)
46: Performance: 8.182 2.933
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.009 0.005 194.5
46: (ns/day) (hour/ns)
46: Performance: 314.124 0.076
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2521 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.301 0.151 199.7
46: (ns/day) (hour/ns)
46: Performance: 9.754 2.461
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.009 0.005 193.8
46: (ns/day) (hour/ns)
46: Performance: 315.265 0.076
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (2492 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.328 0.164 199.6
46: (ns/day) (hour/ns)
46: Performance: 8.942 2.684
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.009 0.005 194.6
46: (ns/day) (hour/ns)
46: Performance: 307.231 0.078
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (2508 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.301 0.151 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.748 2.462
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.009 0.005 194.4
46: (ns/day) (hour/ns)
46: Performance: 311.960 0.077
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (2491 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.269 0.135 199.4
46: (ns/day) (hour/ns)
46: Performance: 10.881 2.206
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 195.4
46: (ns/day) (hour/ns)
46: Performance: 190.495 0.126
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (230 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.259 0.130 199.4
46: (ns/day) (hour/ns)
46: Performance: 11.327 2.119
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 195.5
46: (ns/day) (hour/ns)
46: Performance: 191.038 0.126
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (225 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.243 0.122 199.4
46: (ns/day) (hour/ns)
46: Performance: 12.069 1.989
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 195.5
46: (ns/day) (hour/ns)
46: Performance: 189.248 0.127
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (267 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.243 0.122 199.3
46: (ns/day) (hour/ns)
46: Performance: 12.059 1.990
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 195.1
46: (ns/day) (hour/ns)
46: Performance: 189.446 0.127
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (250 ms)
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (11648 ms total)
46:
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.375 0.188 199.5
46: (ns/day) (hour/ns)
46: Performance: 7.807 3.074
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 151.466 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (289 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.332 0.167 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.817 2.722
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 151.373 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (266 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.299 0.150 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.788 2.452
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 152.080 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (250 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.316 0.158 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.268 2.589
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.3
46: (ns/day) (hour/ns)
46: Performance: 150.284 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (259 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.299 0.150 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.787 2.452
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 151.975 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (249 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.300 0.150 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.764 2.458
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.1
46: (ns/day) (hour/ns)
46: Performance: 151.047 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (250 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.349 0.175 199.5
46: (ns/day) (hour/ns)
46: Performance: 8.383 2.863
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.377 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (275 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.316 0.158 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.272 2.589
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 152.162 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (258 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.316 0.158 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.269 2.589
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 151.945 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (259 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.282 0.141 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.387 2.311
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 151.795 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (242 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.298 0.149 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.826 2.443
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.4
46: (ns/day) (hour/ns)
46: Performance: 152.445 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (249 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.302 0.151 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.699 2.475
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 152.162 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (251 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.301 0.151 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.727 2.467
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.522 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (250 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.317 0.159 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.240 2.597
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 152.309 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (258 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.285 0.143 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.287 2.333
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.500 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (242 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.284 0.142 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.312 2.327
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 152.080 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (241 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.301 0.151 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.740 2.464
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.4
46: (ns/day) (hour/ns)
46: Performance: 152.170 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (250 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.302 0.151 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.699 2.475
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 150.457 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (251 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.316 0.158 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.273 2.588
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 151.597 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (258 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.284 0.143 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.305 2.329
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 152.305 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (241 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.285 0.143 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.304 2.329
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.1
46: (ns/day) (hour/ns)
46: Performance: 152.599 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (242 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.285 0.143 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.291 2.332
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 152.136 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (241 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.345 0.173 199.5
46: (ns/day) (hour/ns)
46: Performance: 8.481 2.830
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 149.918 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (310 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.259 0.130 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.288 2.126
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 150.880 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (267 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.276 0.138 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.606 2.263
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.5
46: (ns/day) (hour/ns)
46: Performance: 150.829 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (275 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.293 0.147 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.998 2.400
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 151.318 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.327 0.164 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.968 2.676
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.686 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (300 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.360 0.180 199.5
46: (ns/day) (hour/ns)
46: Performance: 8.150 2.945
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.2
46: (ns/day) (hour/ns)
46: Performance: 150.622 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (316 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.292 0.147 199.4
46: (ns/day) (hour/ns)
46: Performance: 10.013 2.397
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.054 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (284 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.292 0.146 199.4
46: (ns/day) (hour/ns)
46: Performance: 10.037 2.391
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.7
46: (ns/day) (hour/ns)
46: Performance: 150.854 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.325 0.163 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.012 2.663
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 151.132 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (300 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.258 0.130 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.328 2.119
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 150.604 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (267 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.325 0.163 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.022 2.660
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 150.552 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (300 ms)
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (8756 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 58 tests from 5 test cases ran. (26253 ms total)
46: [ PASSED ] 58 tests.
46/54 Test #46: MdrunNonIntegratorTests ............. Passed 26.29 sec
test 47
Start 47: MdrunTpiTests
47: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTpiTests.xml"
47: Test timeout computed to be: 600
47: [==========] Running 2 tests from 1 test case.
47: [----------] Global test environment set-up.
47: [----------] 2 tests from Simple/TpiTest
47: [ RUN ] Simple/TpiTest.ReproducesOutput/0
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1049 ms)
47: [ RUN ] Simple/TpiTest.ReproducesOutput/1
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (2496 ms)
47: [----------] 2 tests from Simple/TpiTest (3545 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 2 tests from 1 test case ran. (3545 ms total)
47: [ PASSED ] 2 tests.
47/54 Test #47: MdrunTpiTests ....................... Passed 3.57 sec
test 48
Start 48: MdrunMpiTests
48: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
48: Test timeout computed to be: 600
48: [==========] Running 22 tests from 7 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from DomainDecompositionSpecialCasesTest
48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -377490085
48: Generated 3 of the 3 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 3 of the 3 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 9.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.003 0.001 247.0
48: (ns/day) (hour/ns)
48: Performance: 72.856 0.329
48: This run will generate roughly 0 Mb of data
48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (46 ms)
48: [----------] 1 test from DomainDecompositionSpecialCasesTest (46 ms total)
48:
48: [----------] 4 tests from MimicTest
48: [ RUN ] MimicTest.OneQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -806432793
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 355.9
48: (ns/day) (hour/ns)
48: Performance: 57.632 0.416
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.OneQuantumMol (26 ms)
48: [ RUN ] MimicTest.AllQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -1128269892
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 359.4
48: (ns/day) (hour/ns)
48: Performance: 58.388 0.411
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.AllQuantumMol (26 ms)
48: [ RUN ] MimicTest.TwoQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -1074005137
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 357.2
48: (ns/day) (hour/ns)
48: Performance: 59.122 0.406
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.TwoQuantumMol (25 ms)
48: [ RUN ] MimicTest.BondCuts
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 2078113150
48: Generated 2211 of the 2211 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2211 of the 2211 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
48: Number of degrees of freedom in T-Coupling group rest is 66.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: NVE simulation: will use the initial temperature of 300.368 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
48:
48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.007 0.002 367.1
48: (ns/day) (hour/ns)
48: Performance: 47.024 0.510
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.BondCuts (72 ms)
48: [----------] 4 tests from MimicTest (149 ms total)
48:
48: [----------] 1 test from MultiSimTerminationTest
48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from MultiSimTerminationTest (0 ms total)
48:
48: [----------] 3 tests from PmeTest
48: [ RUN ] PmeTest.ReproducesEnergies
48: Setting the LD random seed to -1495343185
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.556 0.140 398.9
48: (ns/day) (hour/ns)
48: Performance: 13.006 1.845
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.664 0.166 399.1
48: (ns/day) (hour/ns)
48: Performance: 10.905 2.201
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.535 0.134 398.9
48: (ns/day) (hour/ns)
48: Performance: 13.534 1.773
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10580 ms)
48: [ RUN ] PmeTest.ScalesTheBox
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -69879809
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.008 0.002 339.1
48: (ns/day) (hour/ns)
48: Performance: 36.326 0.661
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBox (37 ms)
48: [ RUN ] PmeTest.ScalesTheBoxWithWalls
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -268505126
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Searching the wall atom type(s)
48: Number of degrees of freedom in T-Coupling group rest is 13.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: NVE simulation: will use the initial temperature of 966.268 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.027 0.007 372.5
48: (ns/day) (hour/ns)
48: Performance: 12.126 1.979
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBoxWithWalls (30734 ms)
48: [----------] 3 tests from PmeTest (41351 ms total)
48:
48: [----------] 1 test from ReplicaExchangeTerminationTest
48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
48:
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -4.7991020e+01
48: Maximum force = 1.8629866e+02 on atom 13
48: Norm of force = 8.7722033e+01
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2372 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 3.02331e+02 on atom 3
48: F-Norm = 1.18024e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -5.5862247e+01
48: Maximum force = 4.2727914e+02 on atom 13
48: Norm of force = 1.8453180e+02
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2362 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.1937704e+02
48: Maximum force = 9.9988633e+03 on atom 9
48: Norm of force = 4.6166993e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (442 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48:
48: NOTE 3 [file glycine_vacuo.top, line 12]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41575e+04 on atom 10
48: F-Norm = 1.18451e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.5174442e+02
48: Maximum force = 7.4208892e+03 on atom 9
48: Norm of force = 3.5693002e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (444 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.5698419e+02
48: Maximum force = 4.5704996e+02 on atom 17
48: Norm of force = 1.8327748e+02
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (74 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48:
48: NOTE 4 [file unknown]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 5 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 1.06801e+03 on atom 28
48: F-Norm = 4.26916e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.6941193e+02
48: Maximum force = 2.1835349e+02 on atom 17
48: Norm of force = 7.9216550e+01
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (78 ms)
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (5773 ms total)
48:
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents converged to Fmax < 10 in 1 steps
48: Potential Energy = -9.7425699e-01
48: Maximum force = 4.0132303e+00 on atom 3
48: Norm of force = 1.6383944e+00
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (25 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 4.01323e+00 on atom 3
48: F-Norm = 1.63839e+00
48:
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
48: Potential Energy = -9.9064207e-01
48: Maximum force = 2.5781622e+00 on atom 3
48: Norm of force = 1.0525302e+00
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (26 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (12 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.1939685e+02
48: Maximum force = 9.9704248e+03 on atom 9
48: Norm of force = 4.6227568e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (447 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41672e+04 on atom 10
48: F-Norm = 1.19357e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.5625764e+02
48: Maximum force = 7.5018237e+03 on atom 9
48: Norm of force = 3.6139019e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (446 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (426 ms)
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1382 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 22 tests from 7 test cases ran. (48702 ms total)
48: [ PASSED ] 22 tests.
48:
48: YOU HAVE 4 DISABLED TESTS
48:
48/54 Test #48: MdrunMpiTests ....................... Passed 48.73 sec
test 49
Start 49: MdrunMpiCoordinationTestsOneRank
49: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
49: Test timeout computed to be: 960
49: [==========] Running 27 tests from 3 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest
49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.130 0.130 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.273 2.129
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.985 1.716
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.402 1.791
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.501 1.655
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.104 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.182 1.692
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.289 1.680
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (808 ms)
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (808 ms total)
49:
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.093 0.093 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.725 1.526
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.122 0.122 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.009 1.998
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.455 1.927
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.367 1.795
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.104 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.178 1.693
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.112 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.145 1.826
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (791 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.324 1.801
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.922 1.724
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.473 1.781
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.597 1.644
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.252 1.684
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.262 1.957
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (784 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.456 1.927
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.952 1.720
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.109 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.517 1.775
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.624 1.641
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.285 1.680
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.291 1.679
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (775 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.458 1.926
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.931 1.723
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.445 1.928
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.412 1.789
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.095 0.095 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.461 1.552
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.128 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.441 2.098
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (808 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.443 1.662
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.953 1.720
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.476 1.781
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.606 1.643
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.119 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.294 1.952
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.549 1.543
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (767 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.509 1.654
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.959 1.719
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.553 1.771
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.125 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.749 2.043
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.242 1.812
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.591 1.539
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (783 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.159 0.160 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.206 2.607
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.110 1.588
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.488 1.657
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.084 0.085 99.5
49: (ns/day) (hour/ns)
49: Performance: 17.331 1.385
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.095 0.095 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.435 1.555
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.112 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.148 1.825
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (783 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.346 1.798
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.113 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.911 1.859
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.484 1.780
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.608 1.643
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.271 1.682
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.273 1.682
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (775 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.455 1.927
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.147 1.584
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.501 1.778
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.570 1.909
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.239 1.813
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.223 1.815
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (800 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.421 1.788
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.088 0.089 99.7
49: (ns/day) (hour/ns)
49: Performance: 16.544 1.451
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.484 1.657
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.426 1.931
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.211 1.689
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.095 0.095 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.482 1.550
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (749 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.350 1.798
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.088 0.089 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.574 1.448
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.084 0.084 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.479 1.373
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.150 0.151 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.753 2.461
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.128 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.485 2.090
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.281 1.954
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (817 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.134 0.135 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.903 2.201
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.163 0.164 99.8
49: (ns/day) (hour/ns)
49: Performance: 8.981 2.672
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.125 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.728 2.046
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.125 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.733 2.045
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.230 1.814
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.227 1.814
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (908 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.127 0.127 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.532 2.081
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.148 0.148 99.9
49: (ns/day) (hour/ns)
49: Performance: 9.939 2.415
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.305 1.804
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.328 1.801
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.067 1.837
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.066 1.837
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (849 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.361 1.796
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.889 1.862
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.464 1.783
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.516 1.918
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.272 1.956
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.136 0.136 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.776 2.227
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (842 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.354 1.672
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.833 1.870
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.119 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.391 1.937
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.333 1.800
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.104 0.104 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.131 1.698
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.082 1.835
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (792 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.372 1.795
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.948 1.721
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.608 1.643
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.552 1.912
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.119 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.310 1.950
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.194 1.819
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (799 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.135 0.135 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.889 2.204
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.106 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.911 1.725
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.440 1.929
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.426 1.931
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.240 1.961
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.112 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.132 1.828
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (841 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.126 0.127 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.592 2.070
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.130 0.130 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.261 2.131
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.125 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.715 2.049
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.544 1.913
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.216 1.816
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.128 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.486 2.090
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (875 ms)
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (14540 ms total)
49:
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.150 0.150 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.796 2.450
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.758 1.881
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.278 0.279 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.269 4.555
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.128 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.467 2.093
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.143 0.144 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.228 2.347
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.116 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.613 1.903
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (14957 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.125 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.738 2.045
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.887 1.862
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.130 0.130 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.302 2.123
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.133 0.134 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.987 2.184
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.126 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.674 2.056
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.133 0.134 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.995 2.183
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (14740 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.864 1.866
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.134 0.134 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.933 2.195
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.113 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.937 1.855
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.116 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.712 1.888
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.137 0.138 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.667 2.250
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.119 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.337 1.945
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (14723 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.149 0.149 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.835 2.440
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.281 1.954
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.122 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.029 1.995
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.141 0.142 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.353 2.318
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.129 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.407 2.104
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.534 1.915
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (14781 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.287 1.953
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.121 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.157 1.974
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.129 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.412 2.103
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.133 0.133 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.025 2.177
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.127 0.127 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.529 2.082
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.132 0.133 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.060 2.170
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (14755 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.133 0.133 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.047 2.173
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.142 0.142 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.340 2.321
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.140 0.141 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.428 2.302
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.141 0.141 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.391 2.310
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.143 0.144 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.233 2.345
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.138 0.138 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.649 2.254
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (14815 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.127 0.127 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.524 2.083
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.132 0.133 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.078 2.167
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.141 0.141 99.9
49: (ns/day) (hour/ns)
49: Performance: 10.416 2.304
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.139 0.139 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.533 2.279
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.015 1.712
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.121 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.138 1.977
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (14756 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.149 0.149 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.859 2.434
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.133 0.134 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.991 2.184
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.124 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.879 2.020
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.135 0.136 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.834 2.215
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.122 0.122 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.010 1.998
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.107 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.690 1.753
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (14756 ms)
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (118283 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 27 tests from 3 test cases ran. (133631 ms total)
49: [ PASSED ] 27 tests.
49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 133.66 sec
test 50
Start 50: MdrunMpiCoordinationTestsTwoRanks
50: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
50: Test timeout computed to be: 960
50: [==========] Running 27 tests from 3 test cases.
50: [----------] Global test environment set-up.
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest
50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.227 0.114 199.2
50: (ns/day) (hour/ns)
50: Performance: 12.903 1.860
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.253 0.127 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.569 2.074
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.280 0.140 199.3
50: (ns/day) (hour/ns)
50: Performance: 10.470 2.292
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.280 0.140 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.462 2.294
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.251 0.126 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.644 2.061
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.268 0.135 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.914 2.199
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (951 ms)
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (951 ms total)
50:
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.216 0.108 199.2
50: (ns/day) (hour/ns)
50: Performance: 13.543 1.772
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.238 0.119 199.2
50: (ns/day) (hour/ns)
50: Performance: 12.293 1.952
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.247 0.124 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.833 2.028
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.124 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.877 2.021
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.251 0.126 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.653 2.060
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.301 0.151 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.729 2.467
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (900 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.266 0.133 199.3
50: (ns/day) (hour/ns)
50: Performance: 11.017 2.178
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.238 0.119 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.292 1.952
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.911 2.015
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.123 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.903 2.016
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.233 0.117 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.540 1.914
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.217 0.109 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.483 1.780
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (875 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.282 0.141 199.3
50: (ns/day) (hour/ns)
50: Performance: 10.388 2.310
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.270 0.136 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.822 2.218
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.278 0.139 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.532 2.279
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.942 2.010
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.249 0.125 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.737 2.045
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.266 0.134 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.990 2.184
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (950 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.248 0.124 199.3
50: (ns/day) (hour/ns)
50: Performance: 11.802 2.034
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.128 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.501 2.087
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.263 0.132 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.133 2.156
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.124 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.879 2.020
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.234 0.117 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.513 1.918
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.953 2.191
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (908 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.215 0.108 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.576 1.768
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.802 2.222
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.114 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.844 1.869
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.115 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.805 1.874
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.232 0.117 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.573 1.909
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.233 0.117 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.559 1.911
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (859 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.248 0.125 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.795 2.035
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.333 1.674
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.196 2.144
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.244 0.123 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.956 2.007
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.632 1.900
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.670 1.894
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (866 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.248 0.124 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.807 2.033
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.238 0.119 199.2
50: (ns/day) (hour/ns)
50: Performance: 12.305 1.950
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.115 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.717 1.887
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.116 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.700 1.890
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.948 2.192
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.234 0.118 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.491 1.921
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (875 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.677 1.893
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.237 0.119 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.345 1.944
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.211 0.106 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.827 1.736
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.211 0.106 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.823 1.736
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.200 0.100 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.625 1.641
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.216 0.109 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.517 1.776
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (808 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.264 0.133 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.074 2.167
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.103 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.317 1.676
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.227 0.114 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.856 1.867
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.952 2.008
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.282 0.142 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.367 2.315
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.679 1.635
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (867 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.198 0.099 199.1
50: (ns/day) (hour/ns)
50: Performance: 14.772 1.625
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.237 0.119 199.2
50: (ns/day) (hour/ns)
50: Performance: 12.321 1.948
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.213 0.107 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.695 1.752
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.213 0.107 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.707 1.751
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.217 0.109 199.1
50: (ns/day) (hour/ns)
50: Performance: 13.473 1.781
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.235 0.118 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.453 1.927
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (808 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.198 0.100 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.742 1.628
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.356 1.672
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.106 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.807 1.738
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.952 2.008
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.266 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.003 2.181
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.250 0.125 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.712 2.049
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (841 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.214 0.108 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.641 1.759
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.332 1.675
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.195 0.098 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.998 1.600
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.114 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.828 1.871
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.232 0.117 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.569 1.909
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.249 0.125 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.730 2.046
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (817 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.218 0.109 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.433 1.787
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.206 0.104 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.156 1.695
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.669 1.636
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.216 0.108 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.557 1.770
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.187 0.094 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.652 1.533
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.220 0.110 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.294 1.805
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (766 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.232 0.116 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.617 1.902
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.128 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.513 2.085
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.931 2.012
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.295 0.148 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.908 2.422
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.307 0.154 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.548 2.514
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.227 1.963
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1083 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.201 0.101 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.555 1.649
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.223 0.112 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.111 1.831
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.232 0.117 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.608 1.904
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.315 0.158 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.293 2.583
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.203 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.394 1.667
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.236 0.119 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.379 1.939
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (849 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.248 0.124 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.818 2.031
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.128 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.516 2.084
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.946 2.009
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.278 0.140 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.523 2.281
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.266 0.134 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.985 2.185
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.283 0.142 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.350 2.319
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (941 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.266 0.133 199.3
50: (ns/day) (hour/ns)
50: Performance: 11.017 2.178
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.238 0.119 199.2
50: (ns/day) (hour/ns)
50: Performance: 12.306 1.950
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.247 0.124 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.855 2.024
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.124 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.871 2.022
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.251 0.126 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.659 2.058
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.284 0.143 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.302 2.330
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (916 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.265 0.133 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.023 2.177
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.128 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.515 2.084
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.192 2.144
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.262 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.178 2.147
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.249 0.125 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.741 2.044
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.233 0.117 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.550 1.912
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (917 ms)
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (15848 ms total)
50:
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.337 0.169 199.4
50: (ns/day) (hour/ns)
50: Performance: 8.694 2.761
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.285 0.143 199.3
50: (ns/day) (hour/ns)
50: Performance: 10.273 2.336
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.270 0.136 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.820 2.218
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.319 0.160 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.165 2.619
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.283 0.142 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.333 2.323
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.252 0.126 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.612 2.067
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (14933 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.281 0.141 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.405 2.307
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.306 0.154 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.553 2.512
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.276 0.139 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.597 2.265
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.299 0.150 199.1
50: (ns/day) (hour/ns)
50: Performance: 9.781 2.454
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.252 0.127 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.580 2.073
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.237 0.119 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.325 1.947
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (14848 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.259 0.130 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.294 2.125
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.258 1.958
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.277 0.139 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.545 2.276
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.290 0.146 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.090 2.379
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.256 0.128 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.434 2.099
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.256 0.129 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.417 2.102
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (14797 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.240 0.120 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.206 1.966
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.278 0.140 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.507 2.284
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.265 0.133 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.012 2.179
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.269 0.135 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.880 2.206
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.280 0.141 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.445 2.298
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.253 0.127 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.543 2.079
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (14791 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.195 2.144
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.236 0.119 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.388 1.937
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.247 0.124 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.857 2.024
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.219 0.110 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.342 1.799
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.257 0.129 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.396 2.106
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.115 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.826 1.871
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (14713 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.233 0.117 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.525 1.916
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.290 0.146 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.079 2.381
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.250 0.126 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.671 2.056
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.268 0.135 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.901 2.202
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.273 0.137 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.726 2.237
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.223 0.112 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.067 1.837
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (14783 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.896 2.018
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.232 0.117 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.607 1.904
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.304 0.152 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.636 2.491
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.278 0.139 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.534 2.278
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.242 0.121 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.090 1.985
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.255 0.128 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.451 2.096
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (14772 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.797 2.223
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.270 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.822 2.218
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.263 0.132 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.100 2.162
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.217 0.109 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.471 1.782
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.116 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.692 1.891
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.210 1.966
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (14764 ms)
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (118401 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 27 tests from 3 test cases ran. (135201 ms total)
50: [ PASSED ] 27 tests.
50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 135.23 sec
test 51
Start 51: GmxapiExternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 9 tests from 2 test cases.
51: [----------] Global test environment set-up.
51: [----------] 8 tests from GmxApiTest
51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
51: Setting the LD random seed to 2147467199
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.240 0.120 199.4
51: (ns/day) (hour/ns)
51: Performance: 4.212 5.698
51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1006 ms)
51: [ RUN ] GmxApiTest.SystemConstruction
51: Setting the LD random seed to 1032775609
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.SystemConstruction (2319 ms)
51: [ RUN ] GmxApiTest.SaneVersionComparisons
51: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
51: [ RUN ] GmxApiTest.VersionNamed0_1_Features
51: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
51: [ RUN ] GmxApiTest.RunnerBasicMD
51: Setting the LD random seed to -570466371
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.315 0.158 199.5
51: (ns/day) (hour/ns)
51: Performance: 3.201 7.497
51: [ OK ] GmxApiTest.RunnerBasicMD (2480 ms)
51: [ RUN ] GmxApiTest.RunnerReinitialize
51: Setting the LD random seed to -537133225
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51:
51: Received the remote INT/TERM signal, stopping within 50 steps
51:
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.301 0.151 199.5
51: (ns/day) (hour/ns)
51: Performance: 23.496 1.021
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.260 0.130 199.3
51: (ns/day) (hour/ns)
51: Performance: 27.206 0.882
51: [ OK ] GmxApiTest.RunnerReinitialize (2616 ms)
51: [ RUN ] GmxApiTest.RunnerContinuedMD
51: Setting the LD random seed to -90706001
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 10 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.274 0.137 199.4
51: (ns/day) (hour/ns)
51: Performance: 13.519 1.775
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.226 0.113 199.2
51: (ns/day) (hour/ns)
51: Performance: 31.246 0.768
51: [ OK ] GmxApiTest.RunnerContinuedMD (2599 ms)
51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
51: Setting the LD random seed to -310673442
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 1 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.257 0.129 199.5
51: (ns/day) (hour/ns)
51: Performance: 2.620 9.159
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.243 0.122 199.4
51: (ns/day) (hour/ns)
51: Performance: 2.772 8.658
51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (2590 ms)
51: [----------] 8 tests from GmxApiTest (13612 ms total)
51:
51: [----------] 1 test from GmxApiBasicTest
51: [ RUN ] GmxApiBasicTest.Status
51: [ OK ] GmxApiBasicTest.Status (0 ms)
51: [----------] 1 test from GmxApiBasicTest (0 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 9 tests from 2 test cases ran. (13612 ms total)
51: [ PASSED ] 9 tests.
51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 13.64 sec
test 52
Start 52: GmxapiMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 9 tests from 2 test cases.
52: [----------] Global test environment set-up.
52: [----------] 8 tests from GmxApiTest
52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
52: Setting the LD random seed to 1979410814
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.286 0.143 199.5
52: (ns/day) (hour/ns)
52: Performance: 3.536 6.788
52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1024 ms)
52: [ RUN ] GmxApiTest.SystemConstruction
52: Setting the LD random seed to -944931086
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.SystemConstruction (2362 ms)
52: [ RUN ] GmxApiTest.SaneVersionComparisons
52: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
52: [ RUN ] GmxApiTest.VersionNamed0_1_Features
52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
52: [ RUN ] GmxApiTest.RunnerBasicMD
52: Setting the LD random seed to -100663585
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.322 0.161 199.6
52: (ns/day) (hour/ns)
52: Performance: 3.139 7.646
52: [ OK ] GmxApiTest.RunnerBasicMD (2503 ms)
52: [ RUN ] GmxApiTest.RunnerReinitialize
52: Setting the LD random seed to 905869438
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52:
52: Received the remote INT/TERM signal, stopping within 50 steps
52:
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.325 0.163 199.5
52: (ns/day) (hour/ns)
52: Performance: 21.788 1.102
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.259 0.130 199.3
52: (ns/day) (hour/ns)
52: Performance: 27.246 0.881
52: [ OK ] GmxApiTest.RunnerReinitialize (2649 ms)
52: [ RUN ] GmxApiTest.RunnerContinuedMD
52: Setting the LD random seed to -34613473
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 10 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.258 0.129 199.4
52: (ns/day) (hour/ns)
52: Performance: 14.349 1.673
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.242 0.122 199.3
52: (ns/day) (hour/ns)
52: Performance: 29.158 0.823
52: [ OK ] GmxApiTest.RunnerContinuedMD (2617 ms)
52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
52: Setting the LD random seed to -142612865
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 1 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.309 0.155 199.6
52: (ns/day) (hour/ns)
52: Performance: 2.182 11.001
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.5-Raspbian-2020.5-4 (single precision)
52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.259 0.130 199.4
52: (ns/day) (hour/ns)
52: Performance: 2.594 9.251
52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (2649 ms)
52: [----------] 8 tests from GmxApiTest (13805 ms total)
52:
52: [----------] 1 test from GmxApiBasicTest
52: [ RUN ] GmxApiBasicTest.Status
52: [ OK ] GmxApiBasicTest.Status (0 ms)
52: [----------] 1 test from GmxApiBasicTest (0 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 9 tests from 2 test cases ran. (13805 ms total)
52: [ PASSED ] 9 tests.
52/54 Test #52: GmxapiMpiTests ...................... Passed 13.83 sec
test 53
Start 53: GmxapiInternalInterfaceTests
53: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 2 tests from 1 test case.
53: [----------] Global test environment set-up.
53: [----------] 2 tests from GmxApiTest
53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
53: Setting the LD random seed to 1005547263
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (855 ms)
53: [ RUN ] GmxApiTest.CreateApiWorkflow
53: Setting the LD random seed to -687941138
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.CreateApiWorkflow (841 ms)
53: [----------] 2 tests from GmxApiTest (1696 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 2 tests from 1 test case ran. (1696 ms total)
53: [ PASSED ] 2 tests.
53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 1.72 sec
test 54
Start 54: GmxapiInternalsMpiTests
54: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalsMpiTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 2 tests from 1 test case.
54: [----------] Global test environment set-up.
54: [----------] 2 tests from GmxApiTest
54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
54: Setting the LD random seed to 599633403
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (847 ms)
54: [ RUN ] GmxApiTest.CreateApiWorkflow
54: Setting the LD random seed to -1433014465
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.CreateApiWorkflow (839 ms)
54: [----------] 2 tests from GmxApiTest (1686 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 2 tests from 1 test case ran. (1686 ms total)
54: [ PASSED ] 2 tests.
54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 1.71 sec
100% tests passed, 0 tests failed out of 54
Label Time Summary:
GTest = 475.48 sec*proc (54 tests)
IntegrationTest = 179.83 sec*proc (12 tests)
MpiTest = 333.29 sec*proc (8 tests)
SlowTest = 268.89 sec*proc (2 tests)
UnitTest = 26.76 sec*proc (40 tests)
Total Test time (real) = 475.58 sec
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_SingleConstraint_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:331:51: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
331 | std::vector<real> masses = { 1.0, 12.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:333:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
333 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TwoDisjointConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:377:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
377 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:379:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
379 | std::vector<real> constraintsR0 = { 2.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:384:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
384 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:388:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
388 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:390:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
390 | std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:431:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
431 | std::vector<real> constraintsR0 = { 0.1, 0.2 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:438:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
438 | { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:440:101: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
440 | std::vector<RVec> xPrime = { { 0.08, 0.07, 0.01 }, { -0.02, 0.01, -0.02 }, { 0.10, 0.12, 0.11 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:442:85: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
442 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }, { 0.0, 0.0, 1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeConstraintsWithCentralAtom_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:481:61: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
481 | std::vector<real> masses = { 12.0, 1.0, 1.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:483:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
483 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:488:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
488 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:493:59: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
493 | { -0.005, 0.011, 0.102 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:495:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
495 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_FourSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:534:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
534 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:541:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
541 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:545:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
545 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:547:106: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
547 | std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TriangleOfConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:594:63: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
594 | { 0.0, 0.0, oneTenthOverSqrtTwo } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:596:103: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
596 | std::vector<RVec> xPrime = { { 0.09, -0.02, 0.01 }, { -0.02, 0.10, -0.02 }, { 0.03, -0.01, 0.07 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:598:88: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
598 | std::vector<RVec> v = { { 1.0, 1.0, 1.0 }, { -2.0, -2.0, -2.0 }, { 1.0, 1.0, 1.0 } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::ConstraintsTestData::ConstraintsTestData(const string&, int, std::vector<double>, std::vector<int>, std::vector<double>, bool, real (*)[3], bool, float, real, real, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, real, gmx_bool, int, int, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::integrateLeapFrogSimple(gmx::test::LeapFrogTestData*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::SettleTestData::SettleTestData(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<double> gmx::{anonymous}::computeDisplacements(const std::vector<int>&, const std::vector<double>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | updateGroupsCog.addCogs(globalAtomIndices, positions);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::{anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target fft-test
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:79:80: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
79 | 2.86F, 0.24F, 5.76F, 5.19F, 0.72F };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:118:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
118 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:146:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
146 | };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
653 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:325:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
325 | c_sampleCoordinatesFull.begin() + 1);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
328 | c_sampleCoordinatesFull.begin() + 3);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:331:83: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
331 | c_sampleCoordinatesFull.begin() + 16);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp: In function 'void gmx::test::pmeInitAtoms(gmx_pme_t*, gmx::StatePropagatorDataGpu*, gmx::test::CodePath, const CoordinatesVector&, const ChargesVector&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp:201:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target ewald-test
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_identityTransformation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:77:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
77 | translateAndScale(toBeTransformed);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationWithIdentityScaling_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:84:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
84 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingWithZeroTranslation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:94:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
94 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationAndScalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:104:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingIdentity_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:115:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
115 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:125:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
125 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseNoZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:133:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
133 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:134:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
134 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseWithOneScaleDimensionZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:142:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
142 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:143:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target utility-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
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121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
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121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target pbcutil-test
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target math-test
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target pull-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target table-test
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target awh-test
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::{anonymous}::Entropy::runQuasiHarmonic(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::{anonymous}::Entropy::runSchlitter(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target simd-test
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
[ 85%] Built target pdb2gmx1-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::test::AnalysisDataTestInputFrame}; _Tp = gmx::test::AnalysisDataTestInputFrame; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputFrame>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputFrame>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::test::AnalysisDataTestInputFrame& gmx::test::AnalysisDataTestInput::addFrame(real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputFrame*, std::vector<gmx::test::AnalysisDataTestInputFrame> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void gmx::{anonymous}::ExpfitTest::SetUpTestCase()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_IndexOutOfRangeInvalid_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_NoNameFromIncorrectTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFromTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_WrongNameNotFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddTypeWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_EmptyOnCreate_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddMultipleTypesWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CannotAddDuplicateEntry_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target gmxpreprocess-test
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target energyanalysis-test
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp: In member function 'virtual void gmx::test::{anonymous}::MrcDensityMap_ReadsCoordinateTransformationFromFile_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:110:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
110 | coordinateTransformation({ &coordinate1, &coordinate1 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:111:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | coordinateTransformation({ &coordinate2, &coordinate2 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const {anonymous}::NeighborhoodSearchTestData::RefPair&}; _Tp = {anonymous}::NeighborhoodSearchTestData::RefPair; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::RefPair>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::NeighborhoodSearchTestData::computeReferencesInternal(t_pbc*, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double*&}; _Tp = {anonymous}::NeighborhoodSearchTestData::TestPosition; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::TestPosition>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTestData::useRefPositionsAsTestPositions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::AnalysisNeighborhoodPositions {anonymous}::NeighborhoodSearchTestData::testPositions() const':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTest::testPairSearchIndexed(gmx::AnalysisNeighborhood*, const {anonymous}::NeighborhoodSearchTestData&, uint64_t)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static const {anonymous}::NeighborhoodSearchTestData& {anonymous}::RandomBoxXYFullPBCData::get()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchTriclinic_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearch2DPBC_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformNoOriginGiven_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:87:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
87 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchBox_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithOriginDefined_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:106:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithStartValues_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:124:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target fileio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-modules-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
Scanning dependencies of target mdrun-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target mdrun-modules-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-io-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target mdrun-mpi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/dispersion_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-output-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrun-io-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrun-non-integrator-test
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target gmxapi-mpi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target gmxapi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target workflow-details-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::SurfaceAreaTest::generateRandomPositions(int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (15 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (25 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (1 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (1 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (1 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (1 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (5 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (46 ms total)
1: [ PASSED ] 59 tests.
1/54 Test #1: TestUtilsUnitTests .................. Passed 0.07 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (3 ms)
2: [----------] 1 test from MpiSelfTest (4 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (4 ms total)
2: [ PASSED ] 1 test.
2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.02 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 347 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (0 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (1 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (1 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 4 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (0 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
3: [----------] 6 tests from TreeValueTransformTest (2 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (0 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (1 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (2 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms)
3: [----------] 7 tests from LoggerTest (4 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (0 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (0 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (1 ms)
3: [----------] 2 tests from PathTest (2 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (0 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (2 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (0 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (0 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
3: [----------] 10 tests from TextLineWrapperTest (2 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (0 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
3: [----------] 6 tests from TextWriterTest (1 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (0 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 347 tests from 56 test cases ran. (35 ms total)
3: [ PASSED ] 347 tests.
3/54 Test #3: UtilityUnitTests .................... Passed 0.09 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (2 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (2 ms total)
4: [ PASSED ] 2 tests.
4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.02 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 187 tests from 13 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (1 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms)
5: [----------] 2 tests from PrEbinTest (2 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
5: [----------] 4 tests from ShakeTest (0 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (1 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (0 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (0 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (0 ms)
5: [----------] 9 tests from UpdateGroups (0 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms)
5: [----------] 1 test from UpdateGroupsCog (2 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (11 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (5 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (28 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (9 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (9 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (9 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (9 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (110 ms total)
5:
5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (1 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (2 ms total)
5:
5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (1 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (8 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (3 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (38 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (2 ms)
5: [----------] 13 tests from WithParameters/SettleTest (15 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 187 tests from 13 test cases ran. (182 ms total)
5: [ PASSED ] 187 tests.
5/54 Test #5: MdlibUnitTest ....................... Passed 0.22 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (1 ms)
6: [----------] 2 tests from DensityFittingTest (1 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (2 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (0 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (1 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (0 ms)
6: [----------] 3 tests from ElectricFieldTest (1 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (5 ms total)
6: [ PASSED ] 20 tests.
6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.02 sec
test 7
Start 7: CommandLineUnitTests
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 59 tests from 7 test cases.
7: [----------] Global test environment set-up.
7: [----------] 3 tests from CommandLineHelpModuleTest
7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms)
7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (3 ms)
7: [----------] 3 tests from CommandLineHelpModuleTest (5 ms total)
7:
7: [----------] 7 tests from CommandLineHelpWriterTest
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms)
7: [----------] 7 tests from CommandLineHelpWriterTest (3 ms total)
7:
7: [----------] 6 tests from CommandLineModuleManagerTest
7: [ RUN ] CommandLineModuleManagerTest.RunsModule
7: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
7: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total)
7:
7: [----------] 13 tests from CommandLineParserTest
7: [ RUN ] CommandLineParserTest.HandlesSingleValues
7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesString
7: [ OK ] CommandLineParserTest.HandlesString (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
7: [----------] 13 tests from CommandLineParserTest (1 ms total)
7:
7: [----------] 6 tests from CommandLineProgramContextTest
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (1 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
7: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
7:
7: [----------] 3 tests from OutputNamesTest
7: [ RUN ] OutputNamesTest.CanBeSuffixed
7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
7: [----------] 3 tests from OutputNamesTest (0 ms total)
7:
7: [----------] 21 tests from ParseCommonArgsTest
7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (2 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms)
7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
7: [----------] 21 tests from ParseCommonArgsTest (6 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 59 tests from 7 test cases ran. (20 ms total)
7: [ PASSED ] 59 tests.
7/54 Test #7: CommandLineUnitTests ................ Passed 0.04 sec
test 8
Start 8: DomDecTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 9 tests from 2 test cases.
8: [----------] Global test environment set-up.
8: [----------] 7 tests from HashedMap
8: [ RUN ] HashedMap.InsertsFinds
8: [ OK ] HashedMap.InsertsFinds (1 ms)
8: [ RUN ] HashedMap.NegativeKeysWork
8: [ OK ] HashedMap.NegativeKeysWork (0 ms)
8: [ RUN ] HashedMap.InsertsErases
8: [ OK ] HashedMap.InsertsErases (0 ms)
8: [ RUN ] HashedMap.InsertsOrAssigns
8: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
8: [ RUN ] HashedMap.Clears
8: [ OK ] HashedMap.Clears (0 ms)
8: [ RUN ] HashedMap.LinkedEntries
8: [ OK ] HashedMap.LinkedEntries (0 ms)
8: [ RUN ] HashedMap.ResizesTable
8: [ OK ] HashedMap.ResizesTable (0 ms)
8: [----------] 7 tests from HashedMap (1 ms total)
8:
8: [----------] 2 tests from LocalAtomSetManager
8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
8: [----------] 2 tests from LocalAtomSetManager (0 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 9 tests from 2 test cases ran. (1 ms total)
8: [ PASSED ] 9 tests.
8/54 Test #8: DomDecTests ......................... Passed 0.02 sec
test 9
Start 9: EwaldUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 257 tests from 10 test cases.
9: [----------] Global test environment set-up.
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (5 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (7 ms total)
9:
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (10 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (6 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (5 ms)
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (138 ms total)
9:
9: [----------] 144 tests from SaneInput/PmeGatherTest
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms)
9: [----------] 144 tests from SaneInput/PmeGatherTest (142 ms total)
9:
9: [----------] 16 tests from SaneInput/PmeSolveTest
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (3 ms)
9: [----------] 16 tests from SaneInput/PmeSolveTest (48 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (3 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (3 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (17 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (28 ms total)
9:
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (5 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms)
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (46 ms total)
9:
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (5 ms)
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (50 ms total)
9:
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms)
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (66 ms total)
9:
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (14 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (15 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (20 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (21 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (8 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (9 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (13 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (14 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (17 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (20 ms)
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (205 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 257 tests from 10 test cases ran. (771 ms total)
9: [ PASSED ] 257 tests.
9/54 Test #9: EwaldUnitTests ...................... Passed 0.86 sec
test 10
Start 10: FFTUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 14 tests from 4 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from ManyFFTTest
10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (7 ms)
10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (11 ms)
10: [----------] 2 tests from ManyFFTTest (18 ms total)
10:
10: [----------] 1 test from FFTTest
10: [ RUN ] FFTTest.Real2DLength18_15Test
10: [ OK ] FFTTest.Real2DLength18_15Test (4 ms)
10: [----------] 1 test from FFTTest (4 ms total)
10:
10: [----------] 1 test from FFFTest3D
10: [ RUN ] FFFTest3D.Real5_6_9
10: [ OK ] FFFTest3D.Real5_6_9 (3 ms)
10: [----------] 1 test from FFFTest3D (3 ms total)
10:
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (7 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (9 ms)
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (25 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 14 tests from 4 test cases ran. (50 ms total)
10: [ PASSED ] 14 tests.
10/54 Test #10: FFTUnitTests ........................ Passed 0.07 sec
test 11
Start 11: GpuUtilsUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 62 tests from 20 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ClfftInitializer
11: [ RUN ] ClfftInitializer.SingleInitializationWorks
11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
11: [ RUN ] ClfftInitializer.TwoInitializationsWork
11: [ OK ] ClfftInitializer.TwoInitializationsWork (1 ms)
11: [----------] 2 tests from ClfftInitializer (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Swap
11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Comparison
11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Swap
11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Comparison
11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Swap
11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Comparison
11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Swap
11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Comparison
11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/3 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
11:
11: [----------] 1 test from HostAllocatorUntypedTest
11: [ RUN ] HostAllocatorUntypedTest.Comparison
11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/0.Move
11: [ OK ] AllocatorTest/0.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/0 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.Move
11: [ OK ] AllocatorTest/1.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/1 (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/2.Move
11: [ OK ] AllocatorTest/2.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/2 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.Move
11: [ OK ] AllocatorTest/3.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/3 (0 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 62 tests from 20 test cases ran. (5 ms total)
11: [ PASSED ] 62 tests.
11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.03 sec
test 12
Start 12: HardwareUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 4 tests from 1 test case.
12: [----------] Global test environment set-up.
12: [----------] 4 tests from HardwareTopologyTest
12: [ RUN ] HardwareTopologyTest.Execute
12: [ OK ] HardwareTopologyTest.Execute (18 ms)
12: [ RUN ] HardwareTopologyTest.HwlocExecute
12: [ OK ] HardwareTopologyTest.HwlocExecute (17 ms)
12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (18 ms)
12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (17 ms)
12: [----------] 4 tests from HardwareTopologyTest (70 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 4 tests from 1 test case ran. (70 ms total)
12: [ PASSED ] 4 tests.
12/54 Test #12: HardwareUnitTests ................... Passed 0.09 sec
test 13
Start 13: MathUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 204 tests from 29 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from EmptyArrayRefWithPaddingTest
13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
13:
13: [----------] 8 tests from TranslateAndScaleTest
13: [ RUN ] TranslateAndScaleTest.identityTransformation
13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingIdentity
13: [ OK ] TranslateAndScaleTest.scalingIdentity (1 ms)
13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
13: [----------] 8 tests from TranslateAndScaleTest (1 ms total)
13:
13: [----------] 12 tests from DensitySimilarityTest
13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (1 ms)
13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (70 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (71 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (143 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms)
13: [----------] 12 tests from DensitySimilarityTest (288 ms total)
13:
13: [----------] 6 tests from StructureSimilarityTest
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
13: [----------] 6 tests from StructureSimilarityTest (0 ms total)
13:
13: [----------] 8 tests from ExponentialMovingAverage
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
13: [----------] 8 tests from ExponentialMovingAverage (0 ms total)
13:
13: [----------] 21 tests from FunctionTest
13: [ RUN ] FunctionTest.StaticLog2
13: [ OK ] FunctionTest.StaticLog2 (0 ms)
13: [ RUN ] FunctionTest.Log2I32Bit
13: [ OK ] FunctionTest.Log2I32Bit (0 ms)
13: [ RUN ] FunctionTest.Log2I64Bit
13: [ OK ] FunctionTest.Log2I64Bit (0 ms)
13: [ RUN ] FunctionTest.GreatestCommonDivisor
13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
13: [ RUN ] FunctionTest.InvsqrtFloat
13: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvsqrtDouble
13: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvsqrtInteger
13: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
13: [ RUN ] FunctionTest.InvcbrtFloat
13: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvcbrtDouble
13: [ OK ] FunctionTest.InvcbrtDouble (1 ms)
13: [ RUN ] FunctionTest.InvcbrtInteger
13: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
13: [ RUN ] FunctionTest.SixthrootFloat
13: [ OK ] FunctionTest.SixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.SixthrootDouble
13: [ OK ] FunctionTest.SixthrootDouble (0 ms)
13: [ RUN ] FunctionTest.SixthrootInteger
13: [ OK ] FunctionTest.SixthrootInteger (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootFloat
13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootDouble
13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootInteger
13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
13: [ RUN ] FunctionTest.Powers
13: [ OK ] FunctionTest.Powers (0 ms)
13: [ RUN ] FunctionTest.ErfInvFloat
13: [ OK ] FunctionTest.ErfInvFloat (0 ms)
13: [ RUN ] FunctionTest.ErfInvDouble
13: [ OK ] FunctionTest.ErfInvDouble (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
13: [----------] 21 tests from FunctionTest (5 ms total)
13:
13: [----------] 4 tests from GaussianOn1DLattice
13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
13: [ RUN ] GaussianOn1DLattice.isCorrect
13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
13: [----------] 4 tests from GaussianOn1DLattice (0 ms total)
13:
13: [----------] 9 tests from GaussTransformTest
13: [ RUN ] GaussTransformTest.isZeroUponConstruction
13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
13: [ RUN ] GaussTransformTest.view
13: [ OK ] GaussTransformTest.view (0 ms)
13: [----------] 9 tests from GaussTransformTest (2 ms total)
13:
13: [----------] 3 tests from DensityFittingForce
13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
13: [ RUN ] DensityFittingForce.pullsTowardsDerivative
13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
13: [----------] 3 tests from DensityFittingForce (0 ms total)
13:
13: [----------] 2 tests from InvertMatrixTest
13: [ RUN ] InvertMatrixTest.IdentityIsImpotent
13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertMatrixTest.ComputesInverse
13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
13: [----------] 2 tests from InvertMatrixTest (0 ms total)
13:
13: [----------] 2 tests from InvertBoxMatrixTest
13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
13:
13: [----------] 15 tests from MatrixTest
13: [ RUN ] MatrixTest.canSetFromArray
13: [ OK ] MatrixTest.canSetFromArray (0 ms)
13: [ RUN ] MatrixTest.canSetStaticallyFromList
13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
13: [ RUN ] MatrixTest.canConstructAndFill
13: [ OK ] MatrixTest.canConstructAndFill (0 ms)
13: [ RUN ] MatrixTest.canSetValues
13: [ OK ] MatrixTest.canSetValues (0 ms)
13: [ RUN ] MatrixTest.canCopyAssign
13: [ OK ] MatrixTest.canCopyAssign (0 ms)
13: [ RUN ] MatrixTest.canSwap
13: [ OK ] MatrixTest.canSwap (0 ms)
13: [ RUN ] MatrixTest.staticMultiDimArrayExtent
13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MatrixTest.determinantWorks
13: [ OK ] MatrixTest.determinantWorks (0 ms)
13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
13: [ RUN ] MatrixTest.traceWorks
13: [ OK ] MatrixTest.traceWorks (0 ms)
13: [ RUN ] MatrixTest.transposeWorks
13: [ OK ] MatrixTest.transposeWorks (0 ms)
13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
13: [ RUN ] MatrixTest.canFillLegacyMatrix
13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
13: [----------] 15 tests from MatrixTest (1 ms total)
13:
13: [----------] 25 tests from MultiDimArrayTest
13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (1 ms)
13: [ RUN ] MultiDimArrayTest.canSwapStatic
13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapDynamic
13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToView
13: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToConstView
13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
13: [ RUN ] MultiDimArrayTest.viewBegin
13: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.viewEnd
13: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstBegin
13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstEnd
13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
13: [----------] 25 tests from MultiDimArrayTest (1 ms total)
13:
13: [----------] 4 tests from MultiDimArrayToMdSpanTest
13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanCopyAssign
13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanMoveAssign
13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanSwap
13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/0 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanCopyAssign
13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanMoveAssign
13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanSwap
13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanCopyAssign
13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanMoveAssign
13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanSwap
13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanCopyAssign
13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanMoveAssign
13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanSwap
13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/3 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanCopyAssign
13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanMoveAssign
13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanSwap
13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanCopyAssign
13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanMoveAssign
13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanSwap
13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanCopyAssign
13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanMoveAssign
13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanSwap
13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanCopyAssign
13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanMoveAssign
13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanSwap
13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanCopyAssign
13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanMoveAssign
13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanSwap
13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanCopyAssign
13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanMoveAssign
13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanSwap
13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
13:
13: [----------] 37 tests from RVecTest
13: [ RUN ] RVecTest.CanBeStoredInVector
13: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAsMutable_rvec
13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Array
13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
13: [ RUN ] RVecTest.CanAddRVecToRvec
13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanAddAssignRVecToRvec
13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractRVecFromRvec
13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanDotProductRVecByRvec
13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanCrossProductRVecByRvec
13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVecInplace
13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
13: [ RUN ] RVecTest.CanScaleRVec
13: [ OK ] RVecTest.CanScaleRVec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVec
13: [ OK ] RVecTest.CanDivideRVec (0 ms)
13: [ RUN ] RVecTest.CanDoUnitvFromRVec
13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanSqLengthOfRVec
13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanLengthOfRVec
13: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToRVec
13: [ OK ] RVecTest.CanCastToRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToDVec
13: [ OK ] RVecTest.CanCastToDVec (0 ms)
13: [ RUN ] RVecTest.CanLeftScalarMultiply
13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanRightScalarMultiply
13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanGetUnitvFromRVec
13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanGetSqLengthOfRVec
13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanGetLengthOfRVec
13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoCrossProductOfRVec
13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoDotProductOfRVec
13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanScaleByVector
13: [ OK ] RVecTest.CanScaleByVector (0 ms)
13: [ RUN ] RVecTest.asIVec
13: [ OK ] RVecTest.asIVec (0 ms)
13: [ RUN ] RVecTest.elementWiseMin
13: [ OK ] RVecTest.elementWiseMin (0 ms)
13: [ RUN ] RVecTest.elementWiseMax
13: [ OK ] RVecTest.elementWiseMax (0 ms)
13: [ RUN ] RVecTest.WorksAs_dvec_Reference
13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_ivec_Reference
13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Reference
13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
13: [ RUN ] RVecTest.CopyConstructorWorks
13: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
13: [ RUN ] RVecTest.CopyAssignmentWorks
13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
13: [ RUN ] RVecTest.MoveConstructorWorks
13: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
13: [ RUN ] RVecTest.MoveAssignmentWorks
13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
13: [----------] 37 tests from RVecTest (1 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 204 tests from 29 test cases ran. (305 ms total)
13: [ PASSED ] 204 tests.
13/54 Test #13: MathUnitTests ....................... Passed 0.34 sec
test 14
Start 14: MdrunUtilityUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 17 tests from 1 test case.
14: [----------] Global test environment set-up.
14: [----------] 17 tests from ThreadAffinityTest
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
14: NOTE: Affinity setting failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
14: NOTE: Affinity setting for 1/2 threads failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (3 ms)
14: [----------] 17 tests from ThreadAffinityTest (15 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 17 tests from 1 test case ran. (15 ms total)
14: [ PASSED ] 17 tests.
14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.03 sec
test 15
Start 15: MdrunUtilityMpiUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 13 tests from 2 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from ThreadAffinityMultiRankTest
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (6 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (15 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (5 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (3 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
15: [----------] 6 tests from ThreadAffinityMultiRankTest (33 ms total)
15:
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (6 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (7 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (5 ms)
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (38 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 13 tests from 2 test cases ran. (71 ms total)
15: [ PASSED ] 13 tests.
15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 0.09 sec
test 16
Start 16: MDSpanTests
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MDSpanTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 32 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 4 tests from BasicAccessorPolicy
16: [ RUN ] BasicAccessorPolicy.Decay
16: [ OK ] BasicAccessorPolicy.Decay (0 ms)
16: [ RUN ] BasicAccessorPolicy.Access
16: [ OK ] BasicAccessorPolicy.Access (0 ms)
16: [ RUN ] BasicAccessorPolicy.Offset
16: [ OK ] BasicAccessorPolicy.Offset (0 ms)
16: [ RUN ] BasicAccessorPolicy.CopyAccessor
16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
16: [----------] 4 tests from BasicAccessorPolicy (0 ms total)
16:
16: [----------] 4 tests from ExtentsTest
16: [ RUN ] ExtentsTest.Construction
16: [ OK ] ExtentsTest.Construction (0 ms)
16: [ RUN ] ExtentsTest.PurelyStatic
16: [ OK ] ExtentsTest.PurelyStatic (0 ms)
16: [ RUN ] ExtentsTest.RankNought
16: [ OK ] ExtentsTest.RankNought (0 ms)
16: [ RUN ] ExtentsTest.Assignment
16: [ OK ] ExtentsTest.Assignment (0 ms)
16: [----------] 4 tests from ExtentsTest (0 ms total)
16:
16: [----------] 8 tests from MdSpanExtension
16: [ RUN ] MdSpanExtension.SlicingAllStatic
16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingDynamic
16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingAllStatic3D
16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
16: [ RUN ] MdSpanExtension.SlicingEqualsView3D
16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
16: [ RUN ] MdSpanExtension.additionWorks
16: [ OK ] MdSpanExtension.additionWorks (0 ms)
16: [ RUN ] MdSpanExtension.subtractionWorks
16: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
16: [ RUN ] MdSpanExtension.multiplicationWorks
16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
16: [ RUN ] MdSpanExtension.divisionWorks
16: [ OK ] MdSpanExtension.divisionWorks (1 ms)
16: [----------] 8 tests from MdSpanExtension (1 ms total)
16:
16: [----------] 3 tests from LayoutTests
16: [ RUN ] LayoutTests.LayoutRightConstruction
16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
16: [ RUN ] LayoutTests.LayoutRightProperties
16: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
16: [ RUN ] LayoutTests.LayoutRightOperator
16: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
16: [----------] 3 tests from LayoutTests (0 ms total)
16:
16: [----------] 1 test from MdSpanTest
16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
16: [----------] 1 test from MdSpanTest (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
16: [ RUN ] MdSpanTest/0.Rank
16: [ OK ] MdSpanTest/0.Rank (0 ms)
16: [ RUN ] MdSpanTest/0.DynamicRank
16: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/0.Extents
16: [ OK ] MdSpanTest/0.Extents (0 ms)
16: [ RUN ] MdSpanTest/0.Strides
16: [ OK ] MdSpanTest/0.Strides (0 ms)
16: [ RUN ] MdSpanTest/0.Properties
16: [ OK ] MdSpanTest/0.Properties (0 ms)
16: [ RUN ] MdSpanTest/0.Operator
16: [ OK ] MdSpanTest/0.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/0 (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
16: [ RUN ] MdSpanTest/1.Rank
16: [ OK ] MdSpanTest/1.Rank (0 ms)
16: [ RUN ] MdSpanTest/1.DynamicRank
16: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/1.Extents
16: [ OK ] MdSpanTest/1.Extents (0 ms)
16: [ RUN ] MdSpanTest/1.Strides
16: [ OK ] MdSpanTest/1.Strides (0 ms)
16: [ RUN ] MdSpanTest/1.Properties
16: [ OK ] MdSpanTest/1.Properties (0 ms)
16: [ RUN ] MdSpanTest/1.Operator
16: [ OK ] MdSpanTest/1.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/1 (0 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 32 tests from 7 test cases ran. (1 ms total)
16: [ PASSED ] 32 tests.
16/54 Test #16: MDSpanTests ......................... Passed 0.02 sec
test 17
Start 17: OnlineHelpUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 22 tests from 4 test cases.
17: [----------] Global test environment set-up.
17: [----------] 6 tests from TextTableFormatterTest
17: [ RUN ] TextTableFormatterTest.HandlesBasicCase
17: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesIndentation
17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
17: [----------] 6 tests from TextTableFormatterTest (2 ms total)
17:
17: [----------] 3 tests from HelpManagerTest
17: [ RUN ] HelpManagerTest.HandlesRootTopic
17: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
17: [ RUN ] HelpManagerTest.HandlesSubTopics
17: [ OK ] HelpManagerTest.HandlesSubTopics (1 ms)
17: [ RUN ] HelpManagerTest.HandlesInvalidTopics
17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
17: [----------] 3 tests from HelpManagerTest (1 ms total)
17:
17: [----------] 2 tests from HelpTopicFormattingTest
17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
17: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
17:
17: [----------] 11 tests from HelpWriterContextTest
17: [ RUN ] HelpWriterContextTest.FormatsParagraphs
17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralText
17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsBulletList
17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsGridTable
17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsTitles
17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
17: [----------] 11 tests from HelpWriterContextTest (3 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 22 tests from 4 test cases ran. (7 ms total)
17: [ PASSED ] 22 tests.
17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.03 sec
test 18
Start 18: OptionsUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 110 tests from 18 test cases.
18: [----------] Global test environment set-up.
18: [----------] 5 tests from AbstractOptionStorageTest
18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
18: [----------] 5 tests from AbstractOptionStorageTest (2 ms total)
18:
18: [----------] 8 tests from FileNameOptionTest
18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (1 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
18: [----------] 8 tests from FileNameOptionTest (1 ms total)
18:
18: [----------] 15 tests from FileNameOptionManagerTest
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (1 ms)
18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
18: [----------] 15 tests from FileNameOptionManagerTest (2 ms total)
18:
18: [----------] 1 test from OptionsTest
18: [ RUN ] OptionsTest.FailsOnNonsafeStorage
18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
18: [----------] 1 test from OptionsTest (0 ms total)
18:
18: [----------] 9 tests from OptionsAssignerTest
18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMissingValue
18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesExtraValue
18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesGroups
18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesSections
18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
18: [----------] 9 tests from OptionsAssignerTest (1 ms total)
18:
18: [----------] 4 tests from OptionsAssignerBooleanTest
18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total)
18:
18: [----------] 13 tests from OptionsAssignerIntegerTest
18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
18: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total)
18:
18: [----------] 5 tests from OptionsAssignerDoubleTest
18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
18: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
18:
18: [----------] 9 tests from OptionsAssignerStringTest
18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total)
18:
18: [----------] 6 tests from OptionsAssignerEnumTest
18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
18:
18: [----------] 8 tests from RepeatingOptionSectionTest
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
18: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total)
18:
18: [----------] 1 test from TimeUnitManagerTest
18: [ RUN ] TimeUnitManagerTest.BasicOperations
18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
18: [----------] 1 test from TimeUnitManagerTest (0 ms total)
18:
18: [----------] 4 tests from TimeUnitBehaviorTest
18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
18:
18: [----------] 2 tests from TreeValueSupportAssignTest
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (1 ms)
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
18: [----------] 2 tests from TreeValueSupportAssignTest (1 ms total)
18:
18: [----------] 1 test from TreeValueSupportAssignErrorTest
18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
18:
18: [----------] 5 tests from TreeValueSupportCheckTest
18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
18:
18: [----------] 6 tests from TreeValueSupportAdjustTest
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
18: [----------] 6 tests from TreeValueSupportAdjustTest (2 ms total)
18:
18: [----------] 8 tests from TreeValueSupportTest
18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsInt64Option
18: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsStringOption
18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsFloatOption
18: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumOption
18: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
18: [----------] 8 tests from TreeValueSupportTest (3 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 110 tests from 18 test cases ran. (15 ms total)
18: [ PASSED ] 110 tests.
18/54 Test #18: OptionsUnitTests .................... Passed 0.04 sec
test 19
Start 19: PbcutilUnitTest
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml"
19: Test timeout computed to be: 30
19: [==========] Running 3 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 1 test from PbcTest
19: [ RUN ] PbcTest.CalcShiftsWorks
19: [ OK ] PbcTest.CalcShiftsWorks (1 ms)
19: [----------] 1 test from PbcTest (1 ms total)
19:
19: [----------] 2 tests from PbcEnumsTest
19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
19: [----------] 2 tests from PbcEnumsTest (0 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 3 tests from 2 test cases ran. (1 ms total)
19: [ PASSED ] 3 tests.
19/54 Test #19: PbcutilUnitTest ..................... Passed 0.02 sec
test 20
Start 20: RandomUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 44 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 4 tests from ExponentialDistributionTest
20: [ RUN ] ExponentialDistributionTest.Output
20: [ OK ] ExponentialDistributionTest.Output (0 ms)
20: [ RUN ] ExponentialDistributionTest.Logical
20: [ OK ] ExponentialDistributionTest.Logical (0 ms)
20: [ RUN ] ExponentialDistributionTest.Reset
20: [ OK ] ExponentialDistributionTest.Reset (0 ms)
20: [ RUN ] ExponentialDistributionTest.AltParam
20: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from ExponentialDistributionTest (0 ms total)
20:
20: [----------] 4 tests from GammaDistributionTest
20: [ RUN ] GammaDistributionTest.Output
20: [ OK ] GammaDistributionTest.Output (1 ms)
20: [ RUN ] GammaDistributionTest.Logical
20: [ OK ] GammaDistributionTest.Logical (0 ms)
20: [ RUN ] GammaDistributionTest.Reset
20: [ OK ] GammaDistributionTest.Reset (0 ms)
20: [ RUN ] GammaDistributionTest.AltParam
20: [ OK ] GammaDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from GammaDistributionTest (1 ms total)
20:
20: [----------] 4 tests from NormalDistributionTest
20: [ RUN ] NormalDistributionTest.Output
20: [ OK ] NormalDistributionTest.Output (0 ms)
20: [ RUN ] NormalDistributionTest.Logical
20: [ OK ] NormalDistributionTest.Logical (0 ms)
20: [ RUN ] NormalDistributionTest.Reset
20: [ OK ] NormalDistributionTest.Reset (0 ms)
20: [ RUN ] NormalDistributionTest.AltParam
20: [ OK ] NormalDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from NormalDistributionTest (0 ms total)
20:
20: [----------] 1 test from SeedTest
20: [ RUN ] SeedTest.makeRandomSeed
20: [ OK ] SeedTest.makeRandomSeed (0 ms)
20: [----------] 1 test from SeedTest (0 ms total)
20:
20: [----------] 6 tests from TabulatedNormalDistributionTest
20: [ RUN ] TabulatedNormalDistributionTest.Output14
20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Output16
20: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Logical
20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Reset
20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.AltParam
20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
20: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total)
20:
20: [----------] 1 test from TabulatedNormalDistributionTableTest
20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (2 ms)
20: [----------] 1 test from TabulatedNormalDistributionTableTest (2 ms total)
20:
20: [----------] 6 tests from ThreeFry2x64Test
20: [ RUN ] ThreeFry2x64Test.Logical
20: [ OK ] ThreeFry2x64Test.Logical (0 ms)
20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
20: [ RUN ] ThreeFry2x64Test.Reseed
20: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
20: [ RUN ] ThreeFry2x64Test.Discard
20: [ OK ] ThreeFry2x64Test.Discard (0 ms)
20: [ RUN ] ThreeFry2x64Test.InvalidCounter
20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
20: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
20:
20: [----------] 4 tests from UniformIntDistributionTest
20: [ RUN ] UniformIntDistributionTest.Output
20: [ OK ] UniformIntDistributionTest.Output (0 ms)
20: [ RUN ] UniformIntDistributionTest.Logical
20: [ OK ] UniformIntDistributionTest.Logical (0 ms)
20: [ RUN ] UniformIntDistributionTest.Reset
20: [ OK ] UniformIntDistributionTest.Reset (0 ms)
20: [ RUN ] UniformIntDistributionTest.AltParam
20: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from UniformIntDistributionTest (0 ms total)
20:
20: [----------] 5 tests from UniformRealDistributionTest
20: [ RUN ] UniformRealDistributionTest.GenerateCanonical
20: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
20: [ RUN ] UniformRealDistributionTest.Output
20: [ OK ] UniformRealDistributionTest.Output (0 ms)
20: [ RUN ] UniformRealDistributionTest.Logical
20: [ OK ] UniformRealDistributionTest.Logical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Reset
20: [ OK ] UniformRealDistributionTest.Reset (0 ms)
20: [ RUN ] UniformRealDistributionTest.AltParam
20: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
20: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
20:
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (2 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 44 tests from 10 test cases ran. (9 ms total)
20: [ PASSED ] 44 tests.
20/54 Test #20: RandomUnitTests ..................... Passed 0.04 sec
test 21
Start 21: RestraintTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 1 test from 1 test case.
21: [----------] Global test environment set-up.
21: [----------] 1 test from RestraintManager
21: [ RUN ] RestraintManager.restraintList
21: [ OK ] RestraintManager.restraintList (0 ms)
21: [----------] 1 test from RestraintManager (0 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 1 test from 1 test case ran. (1 ms total)
21: [ PASSED ] 1 test.
21/54 Test #21: RestraintTests ...................... Passed 0.02 sec
test 22
Start 22: TableUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 16 tests from 2 test cases.
22: [----------] Global test environment set-up.
22: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms)
22: [ RUN ] SplineTableTest/0.Sinc
22: [ OK ] SplineTableTest/0.Sinc (1 ms)
22: [ RUN ] SplineTableTest/0.LJ12
22: [ OK ] SplineTableTest/0.LJ12 (28 ms)
22: [ RUN ] SplineTableTest/0.PmeCorrection
22: [ OK ] SplineTableTest/0.PmeCorrection (2 ms)
22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms)
22: [ RUN ] SplineTableTest/0.TwoFunctions
22: [ OK ] SplineTableTest/0.TwoFunctions (55 ms)
22: [ RUN ] SplineTableTest/0.ThreeFunctions
22: [ OK ] SplineTableTest/0.ThreeFunctions (63 ms)
22: [----------] 8 tests from SplineTableTest/0 (155 ms total)
22:
22: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (2 ms)
22: [ RUN ] SplineTableTest/1.Sinc
22: [ OK ] SplineTableTest/1.Sinc (4 ms)
22: [ RUN ] SplineTableTest/1.LJ12
22: [ OK ] SplineTableTest/1.LJ12 (66 ms)
22: [ RUN ] SplineTableTest/1.PmeCorrection
22: [ OK ] SplineTableTest/1.PmeCorrection (3 ms)
22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
22: [ RUN ] SplineTableTest/1.TwoFunctions
22: [ OK ] SplineTableTest/1.TwoFunctions (134 ms)
22: [ RUN ] SplineTableTest/1.ThreeFunctions
22: [ OK ] SplineTableTest/1.ThreeFunctions (153 ms)
22: [----------] 8 tests from SplineTableTest/1 (365 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 16 tests from 2 test cases ran. (520 ms total)
22: [ PASSED ] 16 tests.
22/54 Test #22: TableUnitTests ...................... Passed 0.54 sec
test 23
Start 23: TaskAssignmentUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 3 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (1 ms total)
23:
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms)
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 3 tests from 2 test cases ran. (2 ms total)
23: [ PASSED ] 3 tests.
23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.02 sec
test 24
Start 24: TopologyTest
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TopologyTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 11 tests from 3 test cases.
24: [----------] Global test environment set-up.
24: [----------] 3 tests from ExclusionBlockTest
24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (1 ms)
24: [ RUN ] ExclusionBlockTest.MergeExclusions
24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
24: [----------] 3 tests from ExclusionBlockTest (1 ms total)
24:
24: [----------] 2 tests from MtopTest
24: [ RUN ] MtopTest.RangeBasedLoop
24: [ OK ] MtopTest.RangeBasedLoop (0 ms)
24: [ RUN ] MtopTest.Operators
24: [ OK ] MtopTest.Operators (0 ms)
24: [----------] 2 tests from MtopTest (0 ms total)
24:
24: [----------] 6 tests from SymtabTest
24: [ RUN ] SymtabTest.EmptyOnOpen
24: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
24: [ RUN ] SymtabTest.AddSingleEntry
24: [ OK ] SymtabTest.AddSingleEntry (0 ms)
24: [ RUN ] SymtabTest.AddTwoDistinctEntries
24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
24: [ RUN ] SymtabTest.TryToAddDuplicates
24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms)
24: [ RUN ] SymtabTest.AddLargeNumberOfEntries
24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms)
24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms)
24: [----------] 6 tests from SymtabTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 11 tests from 3 test cases ran. (2 ms total)
24: [ PASSED ] 11 tests.
24/54 Test #24: TopologyTest ........................ Passed 0.02 sec
test 25
Start 25: PullTest
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 5 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 5 tests from PullTest
25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
25: [----------] 5 tests from PullTest (0 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 5 tests from 1 test case ran. (0 ms total)
25: [ PASSED ] 5 tests.
25/54 Test #25: PullTest ............................ Passed 0.02 sec
test 26
Start 26: AwhTest
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 12 tests from 4 test cases.
26: [----------] Global test environment set-up.
26: [----------] 1 test from BiasTest
26: [ RUN ] BiasTest.DetectsCovering
26: [ OK ] BiasTest.DetectsCovering (1 ms)
26: [----------] 1 test from BiasTest (1 ms total)
26:
26: [----------] 1 test from gridTest
26: [ RUN ] gridTest.neighborhood
26: [ OK ] gridTest.neighborhood (2 ms)
26: [----------] 1 test from gridTest (2 ms total)
26:
26: [----------] 8 tests from WithParameters/BiasTest
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms)
26: [----------] 8 tests from WithParameters/BiasTest (7 ms total)
26:
26: [----------] 2 tests from WithParameters/BiasStateTest
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms)
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms)
26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 12 tests from 4 test cases ran. (12 ms total)
26: [ PASSED ] 12 tests.
26/54 Test #26: AwhTest ............................. Passed 0.03 sec
test 27
Start 27: SimdUnitTests
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 86 tests from 3 test cases.
27: [----------] Global test environment set-up.
27: [----------] 41 tests from SimdScalarTest
27: [ RUN ] SimdScalarTest.load
27: [ OK ] SimdScalarTest.load (0 ms)
27: [ RUN ] SimdScalarTest.loadU
27: [ OK ] SimdScalarTest.loadU (0 ms)
27: [ RUN ] SimdScalarTest.store
27: [ OK ] SimdScalarTest.store (0 ms)
27: [ RUN ] SimdScalarTest.storeU
27: [ OK ] SimdScalarTest.storeU (0 ms)
27: [ RUN ] SimdScalarTest.setZero
27: [ OK ] SimdScalarTest.setZero (0 ms)
27: [ RUN ] SimdScalarTest.andNot
27: [ OK ] SimdScalarTest.andNot (0 ms)
27: [ RUN ] SimdScalarTest.fma
27: [ OK ] SimdScalarTest.fma (0 ms)
27: [ RUN ] SimdScalarTest.fms
27: [ OK ] SimdScalarTest.fms (0 ms)
27: [ RUN ] SimdScalarTest.fnma
27: [ OK ] SimdScalarTest.fnma (0 ms)
27: [ RUN ] SimdScalarTest.fnms
27: [ OK ] SimdScalarTest.fnms (0 ms)
27: [ RUN ] SimdScalarTest.maskAdd
27: [ OK ] SimdScalarTest.maskAdd (0 ms)
27: [ RUN ] SimdScalarTest.maskzMul
27: [ OK ] SimdScalarTest.maskzMul (0 ms)
27: [ RUN ] SimdScalarTest.maskzFma
27: [ OK ] SimdScalarTest.maskzFma (0 ms)
27: [ RUN ] SimdScalarTest.abs
27: [ OK ] SimdScalarTest.abs (0 ms)
27: [ RUN ] SimdScalarTest.max
27: [ OK ] SimdScalarTest.max (0 ms)
27: [ RUN ] SimdScalarTest.min
27: [ OK ] SimdScalarTest.min (0 ms)
27: [ RUN ] SimdScalarTest.round
27: [ OK ] SimdScalarTest.round (0 ms)
27: [ RUN ] SimdScalarTest.trunc
27: [ OK ] SimdScalarTest.trunc (0 ms)
27: [ RUN ] SimdScalarTest.reduce
27: [ OK ] SimdScalarTest.reduce (0 ms)
27: [ RUN ] SimdScalarTest.testBits
27: [ OK ] SimdScalarTest.testBits (0 ms)
27: [ RUN ] SimdScalarTest.anyTrue
27: [ OK ] SimdScalarTest.anyTrue (0 ms)
27: [ RUN ] SimdScalarTest.selectByMask
27: [ OK ] SimdScalarTest.selectByMask (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMask
27: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
27: [ RUN ] SimdScalarTest.blend
27: [ OK ] SimdScalarTest.blend (0 ms)
27: [ RUN ] SimdScalarTest.cvtR2I
27: [ OK ] SimdScalarTest.cvtR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvttR2I
27: [ OK ] SimdScalarTest.cvttR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvtI2R
27: [ OK ] SimdScalarTest.cvtI2R (0 ms)
27: [ RUN ] SimdScalarTest.cvtF2D
27: [ OK ] SimdScalarTest.cvtF2D (0 ms)
27: [ RUN ] SimdScalarTest.cvtD2D
27: [ OK ] SimdScalarTest.cvtD2D (0 ms)
27: [ RUN ] SimdScalarTest.loadI
27: [ OK ] SimdScalarTest.loadI (0 ms)
27: [ RUN ] SimdScalarTest.loadUI
27: [ OK ] SimdScalarTest.loadUI (0 ms)
27: [ RUN ] SimdScalarTest.storeI
27: [ OK ] SimdScalarTest.storeI (0 ms)
27: [ RUN ] SimdScalarTest.storeUI
27: [ OK ] SimdScalarTest.storeUI (0 ms)
27: [ RUN ] SimdScalarTest.andNotI
27: [ OK ] SimdScalarTest.andNotI (0 ms)
27: [ RUN ] SimdScalarTest.testBitsI
27: [ OK ] SimdScalarTest.testBitsI (0 ms)
27: [ RUN ] SimdScalarTest.selectByMaskI
27: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMaskI
27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
27: [ RUN ] SimdScalarTest.blendI
27: [ OK ] SimdScalarTest.blendI (0 ms)
27: [ RUN ] SimdScalarTest.cvtB2IB
27: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
27: [ RUN ] SimdScalarTest.cvtIB2B
27: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
27: [ RUN ] SimdScalarTest.expandScalarsToTriplets
27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
27: [----------] 41 tests from SimdScalarTest (1 ms total)
27:
27: [----------] 8 tests from SimdScalarUtilTest
27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
27: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
27:
27: [----------] 37 tests from SimdScalarMathTest
27: [ RUN ] SimdScalarMathTest.copysign
27: [ OK ] SimdScalarMathTest.copysign (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPair
27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
27: [ RUN ] SimdScalarMathTest.inv
27: [ OK ] SimdScalarMathTest.inv (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrt
27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
27: [ RUN ] SimdScalarMathTest.log
27: [ OK ] SimdScalarMathTest.log (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2
27: [ OK ] SimdScalarMathTest.exp2 (0 ms)
27: [ RUN ] SimdScalarMathTest.exp
27: [ OK ] SimdScalarMathTest.exp (0 ms)
27: [ RUN ] SimdScalarMathTest.erf
27: [ OK ] SimdScalarMathTest.erf (0 ms)
27: [ RUN ] SimdScalarMathTest.erfc
27: [ OK ] SimdScalarMathTest.erfc (0 ms)
27: [ RUN ] SimdScalarMathTest.sincos
27: [ OK ] SimdScalarMathTest.sincos (0 ms)
27: [ RUN ] SimdScalarMathTest.sin
27: [ OK ] SimdScalarMathTest.sin (0 ms)
27: [ RUN ] SimdScalarMathTest.cos
27: [ OK ] SimdScalarMathTest.cos (0 ms)
27: [ RUN ] SimdScalarMathTest.tan
27: [ OK ] SimdScalarMathTest.tan (0 ms)
27: [ RUN ] SimdScalarMathTest.asin
27: [ OK ] SimdScalarMathTest.asin (0 ms)
27: [ RUN ] SimdScalarMathTest.acos
27: [ OK ] SimdScalarMathTest.acos (0 ms)
27: [ RUN ] SimdScalarMathTest.atan
27: [ OK ] SimdScalarMathTest.atan (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2
27: [ OK ] SimdScalarMathTest.atan2 (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrection
27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.invSingleAccuracy
27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.logSingleAccuracy
27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.expSingleAccuracy
27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
27: [----------] 37 tests from SimdScalarMathTest (1 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 86 tests from 3 test cases ran. (3 ms total)
27: [ PASSED ] 86 tests.
27/54 Test #27: SimdUnitTests ....................... Passed 0.03 sec
test 28
Start 28: CompatibilityHelpersTests
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 170 tests from 12 test cases.
28: [----------] Global test environment set-up.
28: [----------] 45 tests from OptionalTest
28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructEmpty
28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
28: [ RUN ] OptionalTest.CanConstructFromNullopt
28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValue
28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValue
28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (1 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromValue
28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignFromValue
28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanResetContent
28: [ OK ] OptionalTest.CanResetContent (1 ms)
28: [ RUN ] OptionalTest.ProvidesRelationalOperators
28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms)
28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (1 ms)
28: [ RUN ] OptionalTest.CanProduceHash
28: [ OK ] OptionalTest.CanProduceHash (0 ms)
28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
28: alignment_of<char>: 1
28: alignment_of<short>: 2
28: alignment_of<int>: 4
28: alignment_of<long>: 4
28: alignment_of<float>: 4
28: alignment_of<double>: 8
28: alignment_of<long double>: 8
28: alignment_of<Struct>: 1
28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
28: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
28: sizeof( optional<char> ): 2 (1)
28: sizeof( optional<short> ): 4 (2)
28: sizeof( optional<int> ): 8 (4)
28: sizeof( optional<long> ): 8 (4)
28: sizeof( optional<float> ): 8 (4)
28: sizeof( optional<double> ): 16 (8)
28: sizeof( optional<long double> ): 16 (8)
28: sizeof( optional<Struct> ): 2 (1)
28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
28: [----------] 45 tests from OptionalTest (4 ms total)
28:
28: [----------] 7 tests from MakeOptionalTest
28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] MakeOptionalTest.CanCopyConstruct
28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanMoveConstruct
28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
28: [----------] 7 tests from MakeOptionalTest (1 ms total)
28:
28: [----------] 4 tests from OptionalMemberSwapTest
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
28:
28: [----------] 4 tests from OptionalImplicitValueTest
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total)
28:
28: [----------] 20 tests from OptionalIntValueTest
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
28: [----------] 20 tests from OptionalIntValueTest (1 ms total)
28:
28: [----------] 1 test from NotNullConstruction
28: [ RUN ] NotNullConstruction.Works
28: [ OK ] NotNullConstruction.Works (0 ms)
28: [----------] 1 test from NotNullConstruction (0 ms total)
28:
28: [----------] 1 test from NotNullCasting
28: [ RUN ] NotNullCasting.Works
28: [ OK ] NotNullCasting.Works (0 ms)
28: [----------] 1 test from NotNullCasting (0 ms total)
28:
28: [----------] 1 test from NotNullAssignment
28: [ RUN ] NotNullAssignment.Works
28: [ OK ] NotNullAssignment.Works (0 ms)
28: [----------] 1 test from NotNullAssignment (0 ms total)
28:
28: [----------] 1 test from MakeNotNull
28: [ RUN ] MakeNotNull.Works
28: [ OK ] MakeNotNull.Works (0 ms)
28: [----------] 1 test from MakeNotNull (0 ms total)
28:
28: [----------] 1 test from NotNull
28: [ RUN ] NotNull.WorksInContainers
28: [ OK ] NotNull.WorksInContainers (0 ms)
28: [----------] 1 test from NotNull (0 ms total)
28:
28: [----------] 80 tests from StringViewTest
28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromCString
28: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.AllowForwardIteration
28: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstForwardIteration
28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowReverseIteration
28: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstReverseIteration
28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaAt
28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
28: [ RUN ] StringViewTest.CanAccessAllElementsViaData
28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
28: [ RUN ] StringViewTest.CanRemovePrefix
28: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
28: [ RUN ] StringViewTest.CanRemoveSuffix
28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
28: [ RUN ] StringViewTest.CanSwapWithOtherView
28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
28: [ RUN ] StringViewTest.CanCopySubstringWithCopy
28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (1 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (1 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCompareToViews
28: [ OK ] StringViewTest.CanCompareToViews (0 ms)
28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
28: [ RUN ] StringViewTest.CanPrintViewToPutputStream
28: [ OK ] StringViewTest.CanPrintViewToPutputStream (1 ms)
28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
28: [----------] 80 tests from StringViewTest (5 ms total)
28:
28: [----------] 5 tests from StringViewExtensionTest
28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
28: [----------] 5 tests from StringViewExtensionTest (0 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 170 tests from 12 test cases ran. (12 ms total)
28: [ PASSED ] 170 tests.
28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.04 sec
test 29
Start 29: GmxAnaTest
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
29: Test timeout computed to be: 600
29: [==========] Running 27 tests from 5 test cases.
29: [----------] Global test environment set-up.
29: [----------] 5 tests from Entropy
29: [ RUN ] Entropy.Schlitter_300_NoLinear
29: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms)
29: [ RUN ] Entropy.Schlitter_300_Linear
29: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (1 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_Linear
29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
29: [----------] 5 tests from Entropy (1 ms total)
29:
29: [----------] 10 tests from MindistTest
29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (2 ms)
29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (2 ms)
29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (2 ms)
29: [ RUN ] MindistTest.mindistPicksUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistPicksUpContacts (3 ms)
29: [ RUN ] MindistTest.ngWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.ngWorks (2 ms)
29: [ RUN ] MindistTest.groupWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.groupWorks (3 ms)
29: [ RUN ] MindistTest.maxDistWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.maxDistWorks (2 ms)
29: [ RUN ] MindistTest.noPbcWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.noPbcWorks (2 ms)
29: [ RUN ] MindistTest.resPerTimeWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.resPerTimeWorks (3 ms)
29: [ RUN ] MindistTest.matrixWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 5: 'atoms123'
29: Special case: making distance matrix between all atoms in group atoms123
29: [ OK ] MindistTest.matrixWorks (2 ms)
29: [----------] 10 tests from MindistTest (24 ms total)
29:
29: [----------] 3 tests from MsdTest
29: [ RUN ] MsdTest.threeDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.threeDimensionalDiffusion (3 ms)
29: [ RUN ] MsdTest.twoDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.twoDimensionalDiffusion (3 ms)
29: [ RUN ] MsdTest.oneDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.oneDimensionalDiffusion (2 ms)
29: [----------] 3 tests from MsdTest (8 ms total)
29:
29: [----------] 3 tests from MsdMolTest
29: [ RUN ] MsdMolTest.diffMolMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -704657761
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolMassWeighted (1049 ms)
29: [ RUN ] MsdMolTest.diffMolNonMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -2097425
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolNonMassWeighted (1040 ms)
29: [ RUN ] MsdMolTest.diffMolSelected
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -1493632129
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( mol) has 9 elements
29: There is one group in the index
29: Split group of 9 atoms into 3 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolSelected (1043 ms)
29: [----------] 3 tests from MsdMolTest (3132 ms total)
29:
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: trr version: GMX_trn_file (single precision)
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (4 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (5 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (4 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from gro file '', 6 atoms.
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (3 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
29:
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (4 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (3 ms)
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (23 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 27 tests from 5 test cases ran. (3189 ms total)
29: [ PASSED ] 27 tests.
29/54 Test #29: GmxAnaTest .......................... Passed 3.21 sec
test 30
Start 30: GmxPreprocessTests
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 51 tests from 9 test cases.
30: [----------] Global test environment set-up.
30: [----------] 4 tests from GenconfTest
30: [ RUN ] GenconfTest.nbox_Works
30: [ OK ] GenconfTest.nbox_Works (1 ms)
30: [ RUN ] GenconfTest.nbox_norenumber_Works
30: [ OK ] GenconfTest.nbox_norenumber_Works (2 ms)
30: [ RUN ] GenconfTest.nbox_dist_Works
30: [ OK ] GenconfTest.nbox_dist_Works (2 ms)
30: [ RUN ] GenconfTest.nbox_rot_Works
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: [ OK ] GenconfTest.nbox_rot_Works (2 ms)
30: [----------] 4 tests from GenconfTest (7 ms total)
30:
30: [----------] 2 tests from GenionTest
30: [ RUN ] GenionTest.HighConcentrationIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -177054754
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
30: Group 0 ( System) has 653 elements
30: Group 1 ( Water) has 648 elements
30: Group 2 ( SOL) has 648 elements
30: Group 3 ( non-Water) has 5 elements
30: Group 4 ( Other) has 5 elements
30: Group 5 ( METH) has 5 elements
30: Select a group: Number of (3-atomic) solvent molecules: 216
30: Using random seed 1997.
30: Replacing solvent molecule 56 (atom 168) with NA
30: Replacing solvent molecule 120 (atom 360) with NA
30: Replacing solvent molecule 182 (atom 546) with NA
30: Replacing solvent molecule 71 (atom 213) with NA
30: Replacing solvent molecule 189 (atom 567) with CL
30: Replacing solvent molecule 54 (atom 162) with CL
30: Replacing solvent molecule 155 (atom 465) with CL
30: Replacing solvent molecule 99 (atom 297) with CL
30:
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: Will try to add 4 NA ions and 4 CL ions.
30: Select a continuous group of solvent molecules
30: Selected 1: 'Water'
30: [ OK ] GenionTest.HighConcentrationIonPlacement (1073 ms)
30: [ RUN ] GenionTest.NoIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -14226449
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
30: No ions to add, will just copy input configuration.
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: [ OK ] GenionTest.NoIonPlacement (1058 ms)
30: [----------] 2 tests from GenionTest (2131 ms total)
30:
30: [----------] 1 test from GenRestrTest
30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
30:
30: Reading structure file
30: Group 0 ( System) has 156 elements
30: Group 1 ( Protein) has 156 elements
30: Group 2 ( Protein-H) has 75 elements
30: Group 3 ( C-alpha) has 10 elements
30: Group 4 ( Backbone) has 30 elements
30: Group 5 ( MainChain) has 40 elements
30: Group 6 ( MainChain+Cb) has 49 elements
30: Group 7 ( MainChain+H) has 52 elements
30: Group 8 ( SideChain) has 104 elements
30: Group 9 ( SideChain-H) has 35 elements
30: Select a group: Select group to position restrain
30: Selected 3: 'C-alpha'
30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (6 ms)
30: [----------] 1 test from GenRestrTest (6 ms total)
30:
30: [----------] 9 tests from PreprocessingAtomTypesTest
30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total)
30:
30: [----------] 10 tests from PreprocessingBondAtomTypeTest
30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (1 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total)
30:
30: [----------] 5 tests from InsertMoleculesTest
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
30: Added 1 molecules (out of 1 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
30:
30: Output configuration contains 8 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3 success (now 6 atoms)!
30:
Try 4 success (now 8 atoms)!
30:
Try 5 success (now 10 atoms)!
30:
30: Added 5 molecules (out of 5 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
30:
30: Output configuration contains 10 atoms in 10 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
Try 2 success (now 10 atoms)!
30:
30: Added 2 molecules (out of 2 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
30:
30: Output configuration contains 10 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 650 atoms)!
30:
Try 2 success (now 652 atoms)!
30:
Try 3 success (now 654 atoms)!
30:
Try 4 success (now 656 atoms)!
30:
30: Added 4 molecules (out of 4 requested)
30: Replaced 8 residues (24 atoms)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
30:
30: Output configuration contains 632 atoms in 212 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (19 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
30:
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
30:
Try 13 success (now 6 atoms)!
30:
30: Added 3 molecules (out of 4 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
30:
30: Output configuration contains 6 atoms in 3 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (5 ms)
30: [----------] 5 tests from InsertMoleculesTest (36 ms total)
30:
30: [----------] 14 tests from GetIrTest
30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
30: Ignoring obsolete mdp entry 'title'
30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (11 ms)
30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (10 ms)
30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (7 ms)
30: [ RUN ] GetIrTest.RejectsValueWithoutKey
30: [ OK ] GetIrTest.RejectsValueWithoutKey (9 ms)
30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (9 ms)
30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (7 ms)
30: [ RUN ] GetIrTest.AcceptsEmptyLines
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsEmptyLines (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricField
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricField (8 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (7 ms)
30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (3 ms)
30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (7 ms)
30: [ RUN ] GetIrTest.RejectsImplicitSolventYes
30: [ OK ] GetIrTest.RejectsImplicitSolventYes (10 ms)
30: [ RUN ] GetIrTest.AcceptsMimic
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsMimic (7 ms)
30: [----------] 14 tests from GetIrTest (110 ms total)
30:
30: [----------] 5 tests from SolvateTest
30: [ RUN ] SolvateTest.cs_box_Works
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 1x1x1 boxes
30: Solvent box contains 270 atoms in 90 residues
30: Removed 129 solvent atoms due to solvent-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 47 residues
30: Generated solvent containing 141 atoms in 47 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
30:
30: Output configuration contains 141 atoms in 47 residues
30: Volume : 1.331 (nm^3)
30: Density : 1056.36 (g/l)
30: Number of solvent molecules: 47
30:
30: [ OK ] SolvateTest.cs_box_Works (19 ms)
30: [ RUN ] SolvateTest.cs_cp_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: [ OK ] SolvateTest.cs_cp_Works (97 ms)
30: [ RUN ] SolvateTest.cs_cp_p_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: Processing topology
30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
30: [ OK ] SolvateTest.cs_cp_p_Works (98 ms)
30: [ RUN ] SolvateTest.shell_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 1902 solvent atoms more than 1.000000 nm from solute.
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 252 residues
30: Generated solvent containing 756 atoms in 252 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
30:
30: Output configuration contains 762 atoms in 254 residues
30: Volume : 27.2709 (nm^3)
30: Density : 279.3 (g/l)
30: Number of solvent molecules: 252
30:
30: [ OK ] SolvateTest.shell_Works (47 ms)
30: [ RUN ] SolvateTest.update_Topology_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 3x3x3 boxes
30: Solvent box contains 14952 atoms in 4984 residues
30: Removed 2787 solvent atoms due to solvent-solvent overlap
30: Removed 30 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 2 different molecule types:
30: HOH ( 3 atoms): 1876 residues
30: SOL ( 3 atoms): 2169 residues
30: Generated solvent containing 0 atoms in 0 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
30:
30: Output configuration contains 12141 atoms in 4047 residues
30: Volume : 125 (nm^3)
30: Density : 968.963 (g/l)
30: Number of solvent molecules: 4045
30:
30: Processing topology
30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: [ OK ] SolvateTest.update_Topology_Works (389 ms)
30: [----------] 5 tests from SolvateTest (651 ms total)
30:
30: [----------] 1 test from TopDirTests
30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
30: [----------] 1 test from TopDirTests (0 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 51 tests from 9 test cases ran. (2943 ms total)
30: [ PASSED ] 51 tests.
30/54 Test #30: GmxPreprocessTests .................. Passed 2.97 sec
test 31
Start 31: Pdb2gmx1Test
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml"
31: Test timeout computed to be: 30
31: [==========] Running 24 tests from 1 test case.
31: [----------] Global test environment set-up.
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (181 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (186 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (164 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (194 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (215 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (183 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (181 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (203 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (185 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (169 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (196 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (214 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (203 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (181 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (182 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (203 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (184 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (170 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (196 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (214 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (198 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (183 ms)
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (4584 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 24 tests from 1 test case ran. (4584 ms total)
31: [ PASSED ] 24 tests.
31/54 Test #31: Pdb2gmx1Test ........................ Passed 4.61 sec
test 32
Start 32: Pdb2gmx2Test
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 32 tests from 2 test cases.
32: [----------] Global test environment set-up.
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (128 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (143 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (128 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (120 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (130 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (148 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (132 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (124 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (124 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (142 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (127 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (119 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (130 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (148 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (131 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (123 ms)
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (2101 ms total)
32:
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (137 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (155 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (139 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (132 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (141 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (161 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (144 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (135 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (137 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (155 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (139 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (130 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (142 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (160 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (145 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (135 ms)
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (2287 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 32 tests from 2 test cases ran. (4388 ms total)
32: [ PASSED ] 32 tests.
32/54 Test #32: Pdb2gmx2Test ........................ Passed 4.41 sec
test 33
Start 33: Pdb2gmx3Test
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 28 tests from 4 test cases.
33: [----------] Global test environment set-up.
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (175 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (191 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (175 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (157 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (185 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (203 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (190 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (170 ms)
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (1446 ms total)
33:
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (162 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (183 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (166 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (150 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (176 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (195 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (182 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (163 ms)
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (1378 ms total)
33:
33: [----------] 8 tests from ChainSep/Pdb2gmxTest
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (166 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 7 acceptors were found.
33: There are 7 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS8
33: NE223
33: MET12 SD55 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 125, now 125
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 317 pairs
33: Before cleaning: 322 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 5 cmap torsion pairs
33: There are 322 dihedrals, 19 impropers, 227 angles
33: 314 pairs, 125 bonds and 0 virtual sites
33: Total mass 846.083 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 7 58
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (58 atoms, 7 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 7 residues with 124 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 124 atoms 7 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (124 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (165 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 12 acceptors were found.
33: There are 13 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3
33: SG9
33: HIS8 NE251 1.055
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 115, now 115
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 288 pairs
33: Before cleaning: 293 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 6 cmap torsion pairs
33: There are 293 dihedrals, 23 impropers, 203 angles
33: 285 pairs, 115 bonds and 0 virtual sites
33: Total mass 888.952 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 8 61
33: 2 'B' 3 25
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (61 atoms, 8 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 8 residues with 114 atoms
33: Chain time...
33: Processing chain 2 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 114 atoms 8 residues
33: Including chain 2 in system: 61 atoms 3 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (123 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 260, now 260
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 650 pairs
33: Before cleaning: 660 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 8 cmap torsion pairs
33: There are 660 dihedrals, 45 impropers, 466 angles
33: 647 pairs, 260 bonds and 0 virtual sites
33: Total mass 1900.162 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33:
33: Merged chains into joint molecule definitions at 3 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 261 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (167 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 6 donors and 4 acceptors were found.
33: There are 3 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 67, now 67
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 164 pairs
33: Before cleaning: 169 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 169 dihedrals, 13 impropers, 118 angles
33: 161 pairs, 67 bonds and 0 virtual sites
33: Total mass 472.547 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 261 atoms and 16 residues
33: Total mass in system 1900.162 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
33: They will be treated as separate chains unless you reorder your file.
33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 4 33
33: 3 'B' 3 25
33: 4 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (33 atoms, 4 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 66 atoms
33: Chain time...
33: Processing chain 3 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 4 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 66 atoms 4 residues
33: Including chain 3 in system: 61 atoms 3 residues
33: Including chain 4 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (123 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 256, now 256
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 652 pairs
33: Before cleaning: 662 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 12 cmap torsion pairs
33: There are 662 dihedrals, 47 impropers, 460 angles
33: 649 pairs, 256 bonds and 0 virtual sites
33: Total mass 1864.131 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33:
33: Merged chains into joint molecule definitions at 1 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (164 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 14 donors and 15 acceptors were found.
33: There are 20 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 173, now 173
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 441 pairs
33: Before cleaning: 446 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 9 cmap torsion pairs
33: There are 446 dihedrals, 29 impropers, 312 angles
33: 438 pairs, 173 bonds and 0 virtual sites
33: Total mass 1262.488 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 255 atoms and 16 residues
33: Total mass in system 1864.131 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 11 86
33: 2 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (86 atoms, 11 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 11 residues with 172 atoms
33: Chain time...
33: Processing chain 2 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 172 atoms 11 residues
33: Including chain 2 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (127 ms)
33: [----------] 8 tests from ChainSep/Pdb2gmxTest (1160 ms total)
33:
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (83 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (83 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (83 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (83 ms)
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (332 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 28 tests from 4 test cases ran. (4316 ms total)
33: [ PASSED ] 28 tests.
33/54 Test #33: Pdb2gmx3Test ........................ Passed 4.34 sec
test 34
Start 34: CorrelationsTest
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
34: Test timeout computed to be: 30
34: [==========] Running 21 tests from 3 test cases.
34: [----------] Global test environment set-up.
34: [----------] 10 tests from AutocorrTest
34: [ RUN ] AutocorrTest.EacNormal
34: [ OK ] AutocorrTest.EacNormal (12 ms)
34: [ RUN ] AutocorrTest.EacNoNormalize
34: [ OK ] AutocorrTest.EacNoNormalize (8 ms)
34: [ RUN ] AutocorrTest.EacCos
34: [ OK ] AutocorrTest.EacCos (13 ms)
34: [ RUN ] AutocorrTest.EacVector
34: [ OK ] AutocorrTest.EacVector (18 ms)
34: [ RUN ] AutocorrTest.EacRcross
34: [ OK ] AutocorrTest.EacRcross (3 ms)
34: [ RUN ] AutocorrTest.EacP0
34: [ OK ] AutocorrTest.EacP0 (18 ms)
34: [ RUN ] AutocorrTest.EacP1
34: [ OK ] AutocorrTest.EacP1 (18 ms)
34: [ RUN ] AutocorrTest.EacP2
34: [ OK ] AutocorrTest.EacP2 (35 ms)
34: [ RUN ] AutocorrTest.EacP3
34: [ OK ] AutocorrTest.EacP3 (9 ms)
34: [ RUN ] AutocorrTest.EacP4
34: [ OK ] AutocorrTest.EacP4 (19 ms)
34: [----------] 10 tests from AutocorrTest (162 ms total)
34:
34: [----------] 1 test from ManyAutocorrelationTest
34: [ RUN ] ManyAutocorrelationTest.Empty
34: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
34: [----------] 1 test from ManyAutocorrelationTest (1 ms total)
34:
34: [----------] 10 tests from ExpfitTest
34: [ RUN ] ExpfitTest.EffnEXP1
34: [ OK ] ExpfitTest.EffnEXP1 (2 ms)
34: [ RUN ] ExpfitTest.EffnEXP2
34: [ OK ] ExpfitTest.EffnEXP2 (3 ms)
34: [ RUN ] ExpfitTest.EffnEXPEXP
34: [ OK ] ExpfitTest.EffnEXPEXP (4 ms)
34: [ RUN ] ExpfitTest.EffnEXP5
34: [ OK ] ExpfitTest.EffnEXP5 (12 ms)
34: [ RUN ] ExpfitTest.EffnEXP7
34: [ OK ] ExpfitTest.EffnEXP7 (12 ms)
34: [ RUN ] ExpfitTest.EffnEXP9
34: [ OK ] ExpfitTest.EffnEXP9 (41 ms)
34: [ RUN ] ExpfitTest.EffnERF
34: [ OK ] ExpfitTest.EffnERF (8 ms)
34: [ RUN ] ExpfitTest.EffnERREST
34: [ OK ] ExpfitTest.EffnERREST (2 ms)
34: [ RUN ] ExpfitTest.EffnVAC
34: [ OK ] ExpfitTest.EffnVAC (15 ms)
34: [ RUN ] ExpfitTest.EffnPRES
34: [ OK ] ExpfitTest.EffnPRES (39 ms)
34: [----------] 10 tests from ExpfitTest (140 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 21 tests from 3 test cases ran. (334 ms total)
34: [ PASSED ] 21 tests.
34/54 Test #34: CorrelationsTest .................... Passed 0.35 sec
test 35
Start 35: AnalysisDataUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 69 tests from 14 test cases.
35: [----------] Global test environment set-up.
35: [----------] 3 tests from AnalysisDataInitializationTest
35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
35: [----------] 3 tests from AnalysisDataInitializationTest (1 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/0 (25 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (3 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/1 (30 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (3 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (3 ms)
35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/2 (35 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (3 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/3 (35 ms total)
35:
35: [----------] 4 tests from AnalysisArrayDataTest
35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisArrayDataTest.StorageWorks
35: [ OK ] AnalysisArrayDataTest.StorageWorks (3 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
35: [----------] 4 tests from AnalysisArrayDataTest (7 ms total)
35:
35: [----------] 6 tests from AverageModuleTest
35: [ RUN ] AverageModuleTest.BasicTest
35: [ OK ] AverageModuleTest.BasicTest (4 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipointData
35: [ OK ] AverageModuleTest.HandlesMultipointData (5 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeXAxis
35: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
35: [----------] 6 tests from AverageModuleTest (27 ms total)
35:
35: [----------] 2 tests from FrameAverageModuleTest
35: [ RUN ] FrameAverageModuleTest.BasicTest
35: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 2 tests from FrameAverageModuleTest (9 ms total)
35:
35: [----------] 7 tests from AnalysisHistogramSettingsTest
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (1 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
35: [----------] 7 tests from AnalysisHistogramSettingsTest (1 ms total)
35:
35: [----------] 2 tests from SimpleHistogramModuleTest
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [----------] 2 tests from SimpleHistogramModuleTest (13 ms total)
35:
35: [----------] 3 tests from WeightedHistogramModuleTest
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (6 ms)
35: [----------] 3 tests from WeightedHistogramModuleTest (19 ms total)
35:
35: [----------] 3 tests from BinAverageModuleTest
35: [ RUN ] BinAverageModuleTest.ComputesCorrectly
35: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (5 ms)
35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 3 tests from BinAverageModuleTest (16 ms total)
35:
35: [----------] 4 tests from AbstractAverageHistogramTest
35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (11 ms)
35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (6 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (6 ms)
35: [----------] 4 tests from AbstractAverageHistogramTest (30 ms total)
35:
35: [----------] 3 tests from LifetimeModuleTest
35: [ RUN ] LifetimeModuleTest.BasicTest
35: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
35: [ RUN ] LifetimeModuleTest.CumulativeTest
35: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (4 ms)
35: [----------] 3 tests from LifetimeModuleTest (13 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 69 tests from 14 test cases ran. (261 ms total)
35: [ PASSED ] 69 tests.
35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.28 sec
test 36
Start 36: CoordinateIOTests
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 64 tests from 19 test cases.
36: [----------] Global test environment set-up.
36: [----------] 1 test from OutputSelectorDeathTest
36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (12 ms)
36: [----------] 1 test from OutputSelectorDeathTest (12 ms total)
36:
36: [----------] 5 tests from TrajectoryFrameWriterTest
36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (8 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (16 ms)
36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
36: [----------] 5 tests from TrajectoryFrameWriterTest (42 ms total)
36:
36: [----------] 5 tests from OutputAdapterContainer
36: [ RUN ] OutputAdapterContainer.MakeEmpty
36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
36: [ RUN ] OutputAdapterContainer.AddAdapter
36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectBadAdapter
36: [ OK ] OutputAdapterContainer.RejectBadAdapter (1 ms)
36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
36: [----------] 5 tests from OutputAdapterContainer (1 ms total)
36:
36: [----------] 5 tests from FlagTest
36: [ RUN ] FlagTest.CanSetSimpleFlag
36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
36: [ RUN ] FlagTest.CanAddNewBox
36: [ OK ] FlagTest.CanAddNewBox (0 ms)
36: [ RUN ] FlagTest.SetsImplicitPrecisionChange
36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitStartTimeChange
36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitTimeStepChange
36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
36: [----------] 5 tests from FlagTest (0 ms total)
36:
36: [----------] 5 tests from SetAtomsTest
36: [ RUN ] SetAtomsTest.RemovesExistingAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.RemovesExistingAtoms (9 ms)
36: [ RUN ] SetAtomsTest.AddsNewAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.AddsNewAtoms (8 ms)
36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (9 ms)
36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (8 ms)
36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (8 ms)
36: [----------] 5 tests from SetAtomsTest (42 ms total)
36:
36: [----------] 2 tests from SetBothTimeTest
36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (1 ms)
36: [----------] 2 tests from SetBothTimeTest (1 ms total)
36:
36: [----------] 2 tests from SetStartTimeTest
36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
36: [ RUN ] SetStartTimeTest.WorksWithZeroStart
36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
36: [----------] 2 tests from SetStartTimeTest (0 ms total)
36:
36: [----------] 1 test from SetTimeStepTest
36: [ RUN ] SetTimeStepTest.SetTimeStepWorks
36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
36: [----------] 1 test from SetTimeStepTest (0 ms total)
36:
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (8 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (8 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (8 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (8 ms)
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (50 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (8 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (8 ms)
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (25 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
36:
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (17 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (18 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (17 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (18 ms)
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (70 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (8 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (8 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (8 ms)
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (25 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (8 ms)
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (17 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (1 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (8 ms)
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (8 ms)
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (16 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total)
36:
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (8 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (9 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (8 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (9 ms)
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (34 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 64 tests from 19 test cases ran. (338 ms total)
36: [ PASSED ] 64 tests.
36/54 Test #36: CoordinateIOTests ................... Passed 0.36 sec
test 37
Start 37: TrajectoryAnalysisUnitTests
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 82 tests from 16 test cases.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from ClustsizeTest
37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 2, cmax: 4, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (5 ms)
37: [ RUN ] ClustsizeTest.NoMolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 1, cmax: 6, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (5 ms)
37: [ RUN ] ClustsizeTest.MolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (12 ms)
37: [ RUN ] ClustsizeTest.MolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 1, cmax: 6, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms)
37: [ RUN ] ClustsizeTest.MolCSize
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolCSize (12 ms)
37: [----------] 5 tests from ClustsizeTest (46 ms total)
37:
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (8 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (18 ms total)
37:
37: [----------] 11 tests from AngleModuleTest
37: [ RUN ] AngleModuleTest.ComputesSimpleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesSimpleAngles (10 ms)
37: [ RUN ] AngleModuleTest.ComputesDihedrals
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesDihedrals (10 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (10 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
37: Reading frames from gro file 'Test system for different angles', 33 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesMultipleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesMultipleAngles (15 ms)
37: [ RUN ] AngleModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (12 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (14 ms)
37: [----------] 11 tests from AngleModuleTest (127 ms total)
37:
37: [----------] 4 tests from ConvertTrjModuleTest
37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (129 ms)
37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (131 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (10 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (11 ms)
37: [----------] 4 tests from ConvertTrjModuleTest (283 ms total)
37:
37: [----------] 3 tests from DistanceModuleTest
37: [ RUN ] DistanceModuleTest.ComputesDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: [ OK ] DistanceModuleTest.ComputesDistances (13 ms)
37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
37: Number of samples: 4
37: Average distance: 1.81066 nm
37: Standard deviation: 0.79289 nm
37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (17 ms)
37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2 and res_cog x < 2.8:
37: Number of samples: 3
37: Average distance: 1.72076 nm
37: Standard deviation: 1.24839 nm
37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (14 ms)
37: [----------] 3 tests from DistanceModuleTest (45 ms total)
37:
37: [----------] 2 tests from ExtractClusterModuleTest
37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
37: trr version: GMX_trn_file (single precision)
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (12 ms)
37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (13 ms)
37: [----------] 2 tests from ExtractClusterModuleTest (25 ms total)
37:
37: [----------] 2 tests from FreeVolumeModuleTest
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for 40 particles. These were set to zero.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 13
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.02 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
37: Fractional free volume 0.194 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (769 ms)
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 17
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.48 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
37: Fractional free volume 0.200 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (771 ms)
37: [----------] 2 tests from FreeVolumeModuleTest (1540 ms total)
37:
37: [----------] 9 tests from PairDistanceModuleTest
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (10 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (8 ms)
37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (9 ms)
37: [----------] 9 tests from PairDistanceModuleTest (81 ms total)
37:
37: [----------] 5 tests from RdfModuleTest
37: [ RUN ] RdfModuleTest.BasicTest
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.BasicTest (63 ms)
37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (45 ms)
37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (62 ms)
37: [ RUN ] RdfModuleTest.CalculatesSurf
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesSurf (43 ms)
37: [ RUN ] RdfModuleTest.CalculatesXY
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesXY (70 ms)
37: [----------] 5 tests from RdfModuleTest (284 ms total)
37:
37: [----------] 5 tests from SasaModuleTest
37: [ RUN ] SasaModuleTest.BasicTest
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.BasicTest (32 ms)
37: [ RUN ] SasaModuleTest.HandlesSelectedResidues
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesSelectedResidues (20 ms)
37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (17 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (27 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (27 ms)
37: [----------] 5 tests from SasaModuleTest (126 ms total)
37:
37: [----------] 8 tests from SelectModuleTest
37: [ RUN ] SelectModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.BasicTest (18 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (12 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (12 ms)
37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (14 ms)
37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (14 ms)
37: [ RUN ] SelectModuleTest.NormalizesSizes
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.NormalizesSizes (11 ms)
37: [ RUN ] SelectModuleTest.WritesResidueNumbers
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueNumbers (8 ms)
37: [ RUN ] SelectModuleTest.WritesResidueIndices
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueIndices (8 ms)
37: [----------] 8 tests from SelectModuleTest (99 ms total)
37:
37: [----------] 10 tests from SurfaceAreaTest
37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints12
37: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints32
37: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints42
37: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints122
37: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms)
37: [ RUN ] SurfaceAreaTest.Computes100Points
37: [ OK ] SurfaceAreaTest.Computes100Points (2 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (8 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (9 ms)
37: [----------] 10 tests from SurfaceAreaTest (29 ms total)
37:
37: [----------] 4 tests from TopologyInformation
37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
37: [ RUN ] TopologyInformation.WorksWithGroFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithGroFile (9 ms)
37: [ RUN ] TopologyInformation.WorksWithPdbFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithPdbFile (8 ms)
37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1348581426
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
37:
37: NOTE 2 [file lysozyme.top, line 1465]:
37: System has non-zero total charge: 2.000000
37: Total charge should normally be an integer. See
37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
37: for discussion on how close it should be to an integer.
37:
37:
37:
37: Number of degrees of freedom in T-Coupling group rest is 465.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
37: Analysing residue names:
37: There are: 10 Protein residues
37: Analysing Protein...
37: This run will generate roughly 0 Mb of data
37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (1160 ms)
37: [----------] 4 tests from TopologyInformation (1177 ms total)
37:
37: [----------] 4 tests from TrajectoryModuleTest
37: [ RUN ] TrajectoryModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.BasicTest (11 ms)
37: [ RUN ] TrajectoryModuleTest.PlotsXOnly
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.PlotsXOnly (10 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (9 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoForces
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoForces (9 ms)
37: [----------] 4 tests from TrajectoryModuleTest (40 ms total)
37:
37: [----------] 5 tests from UnionFinderTest
37: [ RUN ] UnionFinderTest.WorksEmpty
37: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
37: [ RUN ] UnionFinderTest.BasicMerges
37: [ OK ] UnionFinderTest.BasicMerges (0 ms)
37: [ RUN ] UnionFinderTest.LargerMerges
37: [ OK ] UnionFinderTest.LargerMerges (1 ms)
37: [ RUN ] UnionFinderTest.LongRightMerge
37: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
37: [ RUN ] UnionFinderTest.LongLeftMerge
37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
37: [----------] 5 tests from UnionFinderTest (1 ms total)
37:
37: [----------] 1 test from MappedUnionFinderTest
37: [ RUN ] MappedUnionFinderTest.BasicMerges
37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
37: [----------] 1 test from MappedUnionFinderTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 82 tests from 16 test cases ran. (3922 ms total)
37: [ PASSED ] 82 tests.
37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 3.95 sec
test 38
Start 38: EnergyAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 7 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 1 test from DhdlTest
38: [ RUN ] DhdlTest.ExtractDhdl
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
38: Note: file tpx version 110, software tpx version 119
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
38:
38:
38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
38: [ OK ] DhdlTest.ExtractDhdl (113 ms)
38: [----------] 1 test from DhdlTest (114 ms total)
38:
38: [----------] 1 test from OriresTest
38: [ RUN ] OriresTest.ExtractOrires
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
38: Note: file tpx version 111, software tpx version 119
38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
38: End your selection with 0
38: Selecting all 7 orientation restraints
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
38: [ OK ] OriresTest.ExtractOrires (245 ms)
38: [----------] 1 test from OriresTest (246 ms total)
38:
38: [----------] 3 tests from EnergyTest
38: [ RUN ] EnergyTest.ExtractEnergy
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: [ OK ] EnergyTest.ExtractEnergy (26 ms)
38: [ RUN ] EnergyTest.ExtractEnergyByNumber
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Pres. DC -268.49 3 8.52175 13.2804 (bar)
38: [ OK ] EnergyTest.ExtractEnergyByNumber (27 ms)
38: [ RUN ] EnergyTest.ExtractEnergyMixed
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: [ OK ] EnergyTest.ExtractEnergyMixed (27 ms)
38: [----------] 3 tests from EnergyTest (80 ms total)
38:
38: [----------] 2 tests from ViscosityTest
38: [ RUN ] ViscosityTest.EinsteinViscosity
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosity (45 ms)
38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (42 ms)
38: [----------] 2 tests from ViscosityTest (89 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 7 tests from 4 test cases ran. (529 ms total)
38: [ PASSED ] 7 tests.
38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 0.55 sec
test 39
Start 39: ToolUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 18 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from DumpTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -2093222497
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] DumpTest.WorksWithTpr
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
39: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
39: inputrec:
39: integrator = md
39: tinit = 0
39: dt = 0.001
39: nsteps = 0
39: init-step = 0
39: simulation-part = 1
39: comm-mode = Linear
39: nstcomm = 100
39: bd-fric = 0
39: ld-seed = -2093222497
39: emtol = 10
39: emstep = 0.01
39: niter = 20
39: fcstep = 0
39: nstcgsteep = 1000
39: nbfgscorr = 10
39: rtpi = 0.05
39: nstxout = 0
39: nstvout = 0
39: nstfout = 0
39: nstlog = 1000
39: nstcalcenergy = 100
39: nstenergy = 1000
39: nstxout-compressed = 0
39: compressed-x-precision = 1000
39: cutoff-scheme = Verlet
39: nstlist = 10
39: pbc = xyz
39: periodic-molecules = false
39: verlet-buffer-tolerance = -1
39: rlist = 1.1
39: coulombtype = Cut-off
39: coulomb-modifier = Potential-shift
39: rcoulomb-switch = 0
39: rcoulomb = 1
39: epsilon-r = 1
39: epsilon-rf = inf
39: vdw-type = Cut-off
39: vdw-modifier = Potential-shift
39: rvdw-switch = 0
39: rvdw = 1
39: DispCorr = No
39: table-extension = 1
39: fourierspacing = 0.12
39: fourier-nx = 0
39: fourier-ny = 0
39: fourier-nz = 0
39: pme-order = 4
39: ewald-rtol = 1e-05
39: ewald-rtol-lj = 0.001
39: lj-pme-comb-rule = Geometric
39: ewald-geometry = 0
39: epsilon-surface = 0
39: tcoupl = No
39: nsttcouple = -1
39: nh-chain-length = 0
39: print-nose-hoover-chain-variables = false
39: pcoupl = No
39: pcoupltype = Isotropic
39: nstpcouple = -1
39: tau-p = 1
39: compressibility (3x3):
39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p (3x3):
39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: refcoord-scaling = No
39: posres-com (3):
39: posres-com[0]= 0.00000e+00
39: posres-com[1]= 0.00000e+00
39: posres-com[2]= 0.00000e+00
39: posres-comB (3):
39: posres-comB[0]= 0.00000e+00
39: posres-comB[1]= 0.00000e+00
39: posres-comB[2]= 0.00000e+00
39: QMMM = false
39: QMconstraints = 0
39: QMMMscheme = 0
39: MMChargeScaleFactor = 1
39: qm-opts:
39: ngQM = 0
39: constraint-algorithm = Lincs
39: continuation = false
39: Shake-SOR = false
39: shake-tol = 0.0001
39: lincs-order = 4
39: lincs-iter = 1
39: lincs-warnangle = 30
39: nwall = 0
39: wall-type = 9-3
39: wall-r-linpot = -1
39: wall-atomtype[0] = -1
39: wall-atomtype[1] = -1
39: wall-density[0] = 0
39: wall-density[1] = 0
39: wall-ewald-zfac = 3
39: pull = false
39: awh = false
39: rotation = false
39: interactiveMD = false
39: disre = No
39: disre-weighting = Conservative
39: disre-mixed = false
39: dr-fc = 1000
39: dr-tau = 0
39: nstdisreout = 100
39: orire-fc = 0
39: orire-tau = 0
39: nstorireout = 100
39: free-energy = no
39: cos-acceleration = 0
39: deform (3x3):
39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: simulated-tempering = false
39: swapcoords = no
39: userint1 = 0
39: userint2 = 0
39: userint3 = 0
39: userint4 = 0
39: userreal1 = 0
39: userreal2 = 0
39: userreal3 = 0
39: userreal4 = 0
39: applied-forces:
39: electric-field:
39: x:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: y:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: z:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: density-guided-simulation:
39: active = false
39: group = protein
39: similarity-measure = inner-product
39: atom-spreading-weight = unity
39: force-constant = 1e+09
39: gaussian-transform-spreading-width = 0.2
39: gaussian-transform-spreading-range-in-multiples-of-width = 4
39: reference-density-filename = reference.mrc
39: nst = 1
39: normalize-densities = true
39: adaptive-force-scaling = false
39: adaptive-force-scaling-time-constant = 4
39: grpopts:
39: nrdf: 465
39: ref-t: 0
39: tau-t: 0
39: annealing: No
39: annealing-npoints: 0
39: acc: 0 0 0
39: nfreeze: N N N
39: energygrp-flags[ 0]: 0
39: header:
39: bIr = present
39: bBox = present
39: bTop = present
39: bX = present
39: bV = present
39: bF = not present
39: natoms = 156
39: lambda = 0.000000e+00
39: buffer size = 70122
39: topology:
39: name="First 10 residues from 1AKI"
39: #atoms = 156
39: #molblock = 1
39: molblock (0):
39: moltype = 0 "Protein_chain_B"
39: #molecules = 1
39: #posres_xA = 0
39: #posres_xB = 0
39: bIntermolecularInteractions = false
39: ffparams:
39: atnr=10
39: ntypes=212
39: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06
39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
39: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
39: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
39: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
39: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
39: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
39: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
39: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06
39: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
39: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
39: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
39: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
39: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
39: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
39: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
39: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
39: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08
39: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
39: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
39: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
39: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
39: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
39: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
39: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
39: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
39: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05
39: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
39: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
39: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
39: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
39: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
39: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
39: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
39: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
39: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06
39: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
39: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
39: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
39: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
39: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
39: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
39: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
39: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
39: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06
39: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
39: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
39: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
39: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
39: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
39: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
39: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
39: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
39: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08
39: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
39: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
39: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
39: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
39: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
39: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
39: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
39: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
39: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08
39: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
39: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
39: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
39: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
39: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
39: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
39: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
39: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
39: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05
39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2
39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2
39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2
39: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07
39: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06
39: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06
39: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06
39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
39: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07
39: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06
39: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08
39: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07
39: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06
39: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07
39: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06
39: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06
39: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06
39: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06
39: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07
39: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07
39: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07
39: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06
39: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06
39: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08
39: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07
39: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08
39: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06
39: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07
39: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05
39: reppow = 12
39: fudgeQQ = 0.5
39: cmap
39: atomtypes:
39: atomtype[ 0]={atomnumber= 7}
39: atomtype[ 1]={atomnumber= 1}
39: atomtype[ 2]={atomnumber= 6}
39: atomtype[ 3]={atomnumber= 1}
39: atomtype[ 4]={atomnumber= 6}
39: atomtype[ 5]={atomnumber= 8}
39: atomtype[ 6]={atomnumber= 6}
39: atomtype[ 7]={atomnumber= 1}
39: atomtype[ 8]={atomnumber= 6}
39: atomtype[ 9]={atomnumber= 16}
39: moltype (0):
39: name="Protein_chain_B"
39: atoms:
39: atom (156):
39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
39: atom (156):
39: atom[0]={name="N"}
39: atom[1]={name="H1"}
39: atom[2]={name="H2"}
39: atom[3]={name="H3"}
39: atom[4]={name="CA"}
39: atom[5]={name="HA"}
39: atom[6]={name="CB"}
39: atom[7]={name="HB1"}
39: atom[8]={name="HB2"}
39: atom[9]={name="CG"}
39: atom[10]={name="HG1"}
39: atom[11]={name="HG2"}
39: atom[12]={name="CD"}
39: atom[13]={name="HD1"}
39: atom[14]={name="HD2"}
39: atom[15]={name="CE"}
39: atom[16]={name="HE1"}
39: atom[17]={name="HE2"}
39: atom[18]={name="NZ"}
39: atom[19]={name="HZ1"}
39: atom[20]={name="HZ2"}
39: atom[21]={name="HZ3"}
39: atom[22]={name="C"}
39: atom[23]={name="O"}
39: atom[24]={name="N"}
39: atom[25]={name="H"}
39: atom[26]={name="CA"}
39: atom[27]={name="HA"}
39: atom[28]={name="CB"}
39: atom[29]={name="HB"}
39: atom[30]={name="CG1"}
39: atom[31]={name="HG11"}
39: atom[32]={name="HG12"}
39: atom[33]={name="HG13"}
39: atom[34]={name="CG2"}
39: atom[35]={name="HG21"}
39: atom[36]={name="HG22"}
39: atom[37]={name="HG23"}
39: atom[38]={name="C"}
39: atom[39]={name="O"}
39: atom[40]={name="N"}
39: atom[41]={name="H"}
39: atom[42]={name="CA"}
39: atom[43]={name="HA"}
39: atom[44]={name="CB"}
39: atom[45]={name="HB1"}
39: atom[46]={name="HB2"}
39: atom[47]={name="CG"}
39: atom[48]={name="CD1"}
39: atom[49]={name="HD1"}
39: atom[50]={name="CD2"}
39: atom[51]={name="HD2"}
39: atom[52]={name="CE1"}
39: atom[53]={name="HE1"}
39: atom[54]={name="CE2"}
39: atom[55]={name="HE2"}
39: atom[56]={name="CZ"}
39: atom[57]={name="HZ"}
39: atom[58]={name="C"}
39: atom[59]={name="O"}
39: atom[60]={name="N"}
39: atom[61]={name="H"}
39: atom[62]={name="CA"}
39: atom[63]={name="HA1"}
39: atom[64]={name="HA2"}
39: atom[65]={name="C"}
39: atom[66]={name="O"}
39: atom[67]={name="N"}
39: atom[68]={name="H"}
39: atom[69]={name="CA"}
39: atom[70]={name="HA"}
39: atom[71]={name="CB"}
39: atom[72]={name="HB1"}
39: atom[73]={name="HB2"}
39: atom[74]={name="CG"}
39: atom[75]={name="HG1"}
39: atom[76]={name="HG2"}
39: atom[77]={name="CD"}
39: atom[78]={name="HD1"}
39: atom[79]={name="HD2"}
39: atom[80]={name="NE"}
39: atom[81]={name="HE"}
39: atom[82]={name="CZ"}
39: atom[83]={name="NH1"}
39: atom[84]={name="HH11"}
39: atom[85]={name="HH12"}
39: atom[86]={name="NH2"}
39: atom[87]={name="HH21"}
39: atom[88]={name="HH22"}
39: atom[89]={name="C"}
39: atom[90]={name="O"}
39: atom[91]={name="N"}
39: atom[92]={name="H"}
39: atom[93]={name="CA"}
39: atom[94]={name="HA"}
39: atom[95]={name="CB"}
39: atom[96]={name="HB1"}
39: atom[97]={name="HB2"}
39: atom[98]={name="SG"}
39: atom[99]={name="HG"}
39: atom[100]={name="C"}
39: atom[101]={name="O"}
39: atom[102]={name="N"}
39: atom[103]={name="H"}
39: atom[104]={name="CA"}
39: atom[105]={name="HA"}
39: atom[106]={name="CB"}
39: atom[107]={name="HB1"}
39: atom[108]={name="HB2"}
39: atom[109]={name="CG"}
39: atom[110]={name="HG1"}
39: atom[111]={name="HG2"}
39: atom[112]={name="CD"}
39: atom[113]={name="OE1"}
39: atom[114]={name="OE2"}
39: atom[115]={name="C"}
39: atom[116]={name="O"}
39: atom[117]={name="N"}
39: atom[118]={name="H"}
39: atom[119]={name="CA"}
39: atom[120]={name="HA"}
39: atom[121]={name="CB"}
39: atom[122]={name="HB1"}
39: atom[123]={name="HB2"}
39: atom[124]={name="CG"}
39: atom[125]={name="HG"}
39: atom[126]={name="CD1"}
39: atom[127]={name="HD11"}
39: atom[128]={name="HD12"}
39: atom[129]={name="HD13"}
39: atom[130]={name="CD2"}
39: atom[131]={name="HD21"}
39: atom[132]={name="HD22"}
39: atom[133]={name="HD23"}
39: atom[134]={name="C"}
39: atom[135]={name="O"}
39: atom[136]={name="N"}
39: atom[137]={name="H"}
39: atom[138]={name="CA"}
39: atom[139]={name="HA"}
39: atom[140]={name="CB"}
39: atom[141]={name="HB1"}
39: atom[142]={name="HB2"}
39: atom[143]={name="HB3"}
39: atom[144]={name="C"}
39: atom[145]={name="O"}
39: atom[146]={name="N"}
39: atom[147]={name="H"}
39: atom[148]={name="CA"}
39: atom[149]={name="HA"}
39: atom[150]={name="CB"}
39: atom[151]={name="HB1"}
39: atom[152]={name="HB2"}
39: atom[153]={name="HB3"}
39: atom[154]={name="C"}
39: atom[155]={name="O"}
39: type (156):
39: type[0]={name="opls_287",nameB="opls_287"}
39: type[1]={name="opls_290",nameB="opls_290"}
39: type[2]={name="opls_290",nameB="opls_290"}
39: type[3]={name="opls_290",nameB="opls_290"}
39: type[4]={name="opls_293B",nameB="opls_293B"}
39: type[5]={name="opls_140",nameB="opls_140"}
39: type[6]={name="opls_136",nameB="opls_136"}
39: type[7]={name="opls_140",nameB="opls_140"}
39: type[8]={name="opls_140",nameB="opls_140"}
39: type[9]={name="opls_136",nameB="opls_136"}
39: type[10]={name="opls_140",nameB="opls_140"}
39: type[11]={name="opls_140",nameB="opls_140"}
39: type[12]={name="opls_136",nameB="opls_136"}
39: type[13]={name="opls_140",nameB="opls_140"}
39: type[14]={name="opls_140",nameB="opls_140"}
39: type[15]={name="opls_292",nameB="opls_292"}
39: type[16]={name="opls_140",nameB="opls_140"}
39: type[17]={name="opls_140",nameB="opls_140"}
39: type[18]={name="opls_287",nameB="opls_287"}
39: type[19]={name="opls_290",nameB="opls_290"}
39: type[20]={name="opls_290",nameB="opls_290"}
39: type[21]={name="opls_290",nameB="opls_290"}
39: type[22]={name="opls_235",nameB="opls_235"}
39: type[23]={name="opls_236",nameB="opls_236"}
39: type[24]={name="opls_238",nameB="opls_238"}
39: type[25]={name="opls_241",nameB="opls_241"}
39: type[26]={name="opls_224B",nameB="opls_224B"}
39: type[27]={name="opls_140",nameB="opls_140"}
39: type[28]={name="opls_137",nameB="opls_137"}
39: type[29]={name="opls_140",nameB="opls_140"}
39: type[30]={name="opls_135",nameB="opls_135"}
39: type[31]={name="opls_140",nameB="opls_140"}
39: type[32]={name="opls_140",nameB="opls_140"}
39: type[33]={name="opls_140",nameB="opls_140"}
39: type[34]={name="opls_135",nameB="opls_135"}
39: type[35]={name="opls_140",nameB="opls_140"}
39: type[36]={name="opls_140",nameB="opls_140"}
39: type[37]={name="opls_140",nameB="opls_140"}
39: type[38]={name="opls_235",nameB="opls_235"}
39: type[39]={name="opls_236",nameB="opls_236"}
39: type[40]={name="opls_238",nameB="opls_238"}
39: type[41]={name="opls_241",nameB="opls_241"}
39: type[42]={name="opls_224B",nameB="opls_224B"}
39: type[43]={name="opls_140",nameB="opls_140"}
39: type[44]={name="opls_149",nameB="opls_149"}
39: type[45]={name="opls_140",nameB="opls_140"}
39: type[46]={name="opls_140",nameB="opls_140"}
39: type[47]={name="opls_145",nameB="opls_145"}
39: type[48]={name="opls_145",nameB="opls_145"}
39: type[49]={name="opls_146",nameB="opls_146"}
39: type[50]={name="opls_145",nameB="opls_145"}
39: type[51]={name="opls_146",nameB="opls_146"}
39: type[52]={name="opls_145",nameB="opls_145"}
39: type[53]={name="opls_146",nameB="opls_146"}
39: type[54]={name="opls_145",nameB="opls_145"}
39: type[55]={name="opls_146",nameB="opls_146"}
39: type[56]={name="opls_145",nameB="opls_145"}
39: type[57]={name="opls_146",nameB="opls_146"}
39: type[58]={name="opls_235",nameB="opls_235"}
39: type[59]={name="opls_236",nameB="opls_236"}
39: type[60]={name="opls_238",nameB="opls_238"}
39: type[61]={name="opls_241",nameB="opls_241"}
39: type[62]={name="opls_223B",nameB="opls_223B"}
39: type[63]={name="opls_140",nameB="opls_140"}
39: type[64]={name="opls_140",nameB="opls_140"}
39: type[65]={name="opls_235",nameB="opls_235"}
39: type[66]={name="opls_236",nameB="opls_236"}
39: type[67]={name="opls_238",nameB="opls_238"}
39: type[68]={name="opls_241",nameB="opls_241"}
39: type[69]={name="opls_224B",nameB="opls_224B"}
39: type[70]={name="opls_140",nameB="opls_140"}
39: type[71]={name="opls_136",nameB="opls_136"}
39: type[72]={name="opls_140",nameB="opls_140"}
39: type[73]={name="opls_140",nameB="opls_140"}
39: type[74]={name="opls_308",nameB="opls_308"}
39: type[75]={name="opls_140",nameB="opls_140"}
39: type[76]={name="opls_140",nameB="opls_140"}
39: type[77]={name="opls_307",nameB="opls_307"}
39: type[78]={name="opls_140",nameB="opls_140"}
39: type[79]={name="opls_140",nameB="opls_140"}
39: type[80]={name="opls_303",nameB="opls_303"}
39: type[81]={name="opls_304",nameB="opls_304"}
39: type[82]={name="opls_302",nameB="opls_302"}
39: type[83]={name="opls_300",nameB="opls_300"}
39: type[84]={name="opls_301",nameB="opls_301"}
39: type[85]={name="opls_301",nameB="opls_301"}
39: type[86]={name="opls_300",nameB="opls_300"}
39: type[87]={name="opls_301",nameB="opls_301"}
39: type[88]={name="opls_301",nameB="opls_301"}
39: type[89]={name="opls_235",nameB="opls_235"}
39: type[90]={name="opls_236",nameB="opls_236"}
39: type[91]={name="opls_238",nameB="opls_238"}
39: type[92]={name="opls_241",nameB="opls_241"}
39: type[93]={name="opls_224B",nameB="opls_224B"}
39: type[94]={name="opls_140",nameB="opls_140"}
39: type[95]={name="opls_206",nameB="opls_206"}
39: type[96]={name="opls_140",nameB="opls_140"}
39: type[97]={name="opls_140",nameB="opls_140"}
39: type[98]={name="opls_200",nameB="opls_200"}
39: type[99]={name="opls_204",nameB="opls_204"}
39: type[100]={name="opls_235",nameB="opls_235"}
39: type[101]={name="opls_236",nameB="opls_236"}
39: type[102]={name="opls_238",nameB="opls_238"}
39: type[103]={name="opls_241",nameB="opls_241"}
39: type[104]={name="opls_224B",nameB="opls_224B"}
39: type[105]={name="opls_140",nameB="opls_140"}
39: type[106]={name="opls_136",nameB="opls_136"}
39: type[107]={name="opls_140",nameB="opls_140"}
39: type[108]={name="opls_140",nameB="opls_140"}
39: type[109]={name="opls_274",nameB="opls_274"}
39: type[110]={name="opls_140",nameB="opls_140"}
39: type[111]={name="opls_140",nameB="opls_140"}
39: type[112]={name="opls_271",nameB="opls_271"}
39: type[113]={name="opls_272",nameB="opls_272"}
39: type[114]={name="opls_272",nameB="opls_272"}
39: type[115]={name="opls_235",nameB="opls_235"}
39: type[116]={name="opls_236",nameB="opls_236"}
39: type[117]={name="opls_238",nameB="opls_238"}
39: type[118]={name="opls_241",nameB="opls_241"}
39: type[119]={name="opls_224B",nameB="opls_224B"}
39: type[120]={name="opls_140",nameB="opls_140"}
39: type[121]={name="opls_136",nameB="opls_136"}
39: type[122]={name="opls_140",nameB="opls_140"}
39: type[123]={name="opls_140",nameB="opls_140"}
39: type[124]={name="opls_137",nameB="opls_137"}
39: type[125]={name="opls_140",nameB="opls_140"}
39: type[126]={name="opls_135",nameB="opls_135"}
39: type[127]={name="opls_140",nameB="opls_140"}
39: type[128]={name="opls_140",nameB="opls_140"}
39: type[129]={name="opls_140",nameB="opls_140"}
39: type[130]={name="opls_135",nameB="opls_135"}
39: type[131]={name="opls_140",nameB="opls_140"}
39: type[132]={name="opls_140",nameB="opls_140"}
39: type[133]={name="opls_140",nameB="opls_140"}
39: type[134]={name="opls_235",nameB="opls_235"}
39: type[135]={name="opls_236",nameB="opls_236"}
39: type[136]={name="opls_238",nameB="opls_238"}
39: type[137]={name="opls_241",nameB="opls_241"}
39: type[138]={name="opls_224B",nameB="opls_224B"}
39: type[139]={name="opls_140",nameB="opls_140"}
39: type[140]={name="opls_135",nameB="opls_135"}
39: type[141]={name="opls_140",nameB="opls_140"}
39: type[142]={name="opls_140",nameB="opls_140"}
39: type[143]={name="opls_140",nameB="opls_140"}
39: type[144]={name="opls_235",nameB="opls_235"}
39: type[145]={name="opls_236",nameB="opls_236"}
39: type[146]={name="opls_238",nameB="opls_238"}
39: type[147]={name="opls_241",nameB="opls_241"}
39: type[148]={name="opls_224B",nameB="opls_224B"}
39: type[149]={name="opls_140",nameB="opls_140"}
39: type[150]={name="opls_135",nameB="opls_135"}
39: type[151]={name="opls_140",nameB="opls_140"}
39: type[152]={name="opls_140",nameB="opls_140"}
39: type[153]={name="opls_140",nameB="opls_140"}
39: type[154]={name="opls_235",nameB="opls_235"}
39: type[155]={name="opls_236",nameB="opls_236"}
39: residue (10):
39: residue[0]={name="LYS", nr=1, ic=' '}
39: residue[1]={name="VAL", nr=2, ic=' '}
39: residue[2]={name="PHE", nr=3, ic=' '}
39: residue[3]={name="GLY", nr=4, ic=' '}
39: residue[4]={name="ARG", nr=5, ic=' '}
39: residue[5]={name="CYS", nr=6, ic=' '}
39: residue[6]={name="GLU", nr=7, ic=' '}
39: residue[7]={name="LEU", nr=8, ic=' '}
39: residue[8]={name="ALA", nr=9, ic=' '}
39: residue[9]={name="ALA", nr=10, ic=' '}
39: excls:
39: nr=156
39: nra=1828
39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
39: 23, 24, 25, 26}
39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
39: 14, 15, 22, 23, 24}
39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
39: 16, 17, 18, 22}
39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
39: 17, 18, 19, 20, 21}
39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
39: 19, 20, 21}
39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
39: 25, 26, 27, 28, 38}
39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
39: 30, 34, 38, 39, 40}
39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40}
39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
39: 34, 35, 36, 37, 38, 39, 40}
39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40, 41, 42, 43, 44, 58}
39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
39: 45, 46, 47, 58, 59, 60}
39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
39: 48, 50, 58, 59, 60, 61, 62}
39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60}
39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
39: 50, 51, 52, 54, 58, 59, 60}
39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
39: 52, 53, 54, 55, 56, 58}
39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
39: 54, 56, 57}
39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
39: 55, 56, 57}
39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60, 61, 62, 63, 64, 65}
39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
39: 65, 66, 67}
39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
39: 68, 69}
39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
39: 70, 71, 89}
39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
39: 72, 73, 74, 89, 90, 91}
39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
39: 75, 76, 77, 89, 90, 91, 92, 93}
39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
39: 91}
39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
39: 77, 78, 79, 80, 89, 90, 91}
39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
39: 79, 80, 81, 82, 89}
39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
39: 81, 82, 83, 86}
39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
39: 84, 85, 86, 87, 88}
39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
39: 86, 87, 88}
39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
39: 90, 91, 92, 93, 94, 95, 100}
39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
39: 95, 96, 97, 98, 100, 101, 102}
39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
39: 98, 99, 100, 101, 102, 103, 104}
39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102}
39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
39: 100, 101, 102}
39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102, 103, 104, 105, 106, 115}
39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
39: 105, 106, 107, 108, 109, 115, 116, 117}
39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
39: 115}
39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117}
39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 110, 111, 112, 113, 114, 115, 116, 117}
39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 113, 114, 115}
39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117, 118, 119, 120, 121, 134}
39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119}
39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119, 120, 121, 122, 123, 124, 134, 135, 136}
39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
39: 134}
39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136}
39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
39: 136}
39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 127, 128, 129, 130, 131, 132, 133, 134}
39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136, 137, 138, 139, 140, 144}
39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138}
39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138, 139, 140, 141, 142, 143, 144, 145, 146}
39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
39: 144}
39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
39: 141, 142, 143, 144, 145, 146, 147, 148}
39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146, 147, 148, 149, 150, 154}
39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148}
39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148, 149, 150, 151, 152, 153, 154, 155}
39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
39: 154}
39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
39: 151, 152, 153, 154, 155}
39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
39: Bond:
39: nr: 468
39: iatoms:
39: 0 type=100 (BONDS) 0 1
39: 1 type=100 (BONDS) 0 2
39: 2 type=100 (BONDS) 0 3
39: 3 type=101 (BONDS) 0 4
39: 4 type=102 (BONDS) 4 5
39: 5 type=103 (BONDS) 4 6
39: 6 type=104 (BONDS) 4 22
39: 7 type=102 (BONDS) 6 7
39: 8 type=102 (BONDS) 6 8
39: 9 type=103 (BONDS) 6 9
39: 10 type=102 (BONDS) 9 10
39: 11 type=102 (BONDS) 9 11
39: 12 type=103 (BONDS) 9 12
39: 13 type=102 (BONDS) 12 13
39: 14 type=102 (BONDS) 12 14
39: 15 type=103 (BONDS) 12 15
39: 16 type=102 (BONDS) 15 16
39: 17 type=102 (BONDS) 15 17
39: 18 type=101 (BONDS) 15 18
39: 19 type=100 (BONDS) 18 19
39: 20 type=100 (BONDS) 18 20
39: 21 type=100 (BONDS) 18 21
39: 22 type=105 (BONDS) 22 23
39: 23 type=106 (BONDS) 22 24
39: 24 type=100 (BONDS) 24 25
39: 25 type=107 (BONDS) 24 26
39: 26 type=102 (BONDS) 26 27
39: 27 type=103 (BONDS) 26 28
39: 28 type=104 (BONDS) 26 38
39: 29 type=102 (BONDS) 28 29
39: 30 type=103 (BONDS) 28 30
39: 31 type=103 (BONDS) 28 34
39: 32 type=102 (BONDS) 30 31
39: 33 type=102 (BONDS) 30 32
39: 34 type=102 (BONDS) 30 33
39: 35 type=102 (BONDS) 34 35
39: 36 type=102 (BONDS) 34 36
39: 37 type=102 (BONDS) 34 37
39: 38 type=105 (BONDS) 38 39
39: 39 type=106 (BONDS) 38 40
39: 40 type=100 (BONDS) 40 41
39: 41 type=107 (BONDS) 40 42
39: 42 type=102 (BONDS) 42 43
39: 43 type=103 (BONDS) 42 44
39: 44 type=104 (BONDS) 42 58
39: 45 type=102 (BONDS) 44 45
39: 46 type=102 (BONDS) 44 46
39: 47 type=108 (BONDS) 44 47
39: 48 type=109 (BONDS) 47 48
39: 49 type=109 (BONDS) 47 50
39: 50 type=110 (BONDS) 48 49
39: 51 type=109 (BONDS) 48 52
39: 52 type=110 (BONDS) 50 51
39: 53 type=109 (BONDS) 50 54
39: 54 type=110 (BONDS) 52 53
39: 55 type=109 (BONDS) 52 56
39: 56 type=110 (BONDS) 54 55
39: 57 type=109 (BONDS) 54 56
39: 58 type=110 (BONDS) 56 57
39: 59 type=105 (BONDS) 58 59
39: 60 type=106 (BONDS) 58 60
39: 61 type=100 (BONDS) 60 61
39: 62 type=107 (BONDS) 60 62
39: 63 type=102 (BONDS) 62 63
39: 64 type=102 (BONDS) 62 64
39: 65 type=104 (BONDS) 62 65
39: 66 type=105 (BONDS) 65 66
39: 67 type=106 (BONDS) 65 67
39: 68 type=100 (BONDS) 67 68
39: 69 type=107 (BONDS) 67 69
39: 70 type=102 (BONDS) 69 70
39: 71 type=103 (BONDS) 69 71
39: 72 type=104 (BONDS) 69 89
39: 73 type=102 (BONDS) 71 72
39: 74 type=102 (BONDS) 71 73
39: 75 type=103 (BONDS) 71 74
39: 76 type=102 (BONDS) 74 75
39: 77 type=102 (BONDS) 74 76
39: 78 type=103 (BONDS) 74 77
39: 79 type=102 (BONDS) 77 78
39: 80 type=102 (BONDS) 77 79
39: 81 type=111 (BONDS) 77 80
39: 82 type=100 (BONDS) 80 81
39: 83 type=112 (BONDS) 80 82
39: 84 type=112 (BONDS) 82 83
39: 85 type=112 (BONDS) 82 86
39: 86 type=100 (BONDS) 83 84
39: 87 type=100 (BONDS) 83 85
39: 88 type=100 (BONDS) 86 87
39: 89 type=100 (BONDS) 86 88
39: 90 type=105 (BONDS) 89 90
39: 91 type=106 (BONDS) 89 91
39: 92 type=100 (BONDS) 91 92
39: 93 type=107 (BONDS) 91 93
39: 94 type=102 (BONDS) 93 94
39: 95 type=103 (BONDS) 93 95
39: 96 type=104 (BONDS) 93 100
39: 97 type=102 (BONDS) 95 96
39: 98 type=102 (BONDS) 95 97
39: 99 type=113 (BONDS) 95 98
39: 100 type=114 (BONDS) 98 99
39: 101 type=105 (BONDS) 100 101
39: 102 type=106 (BONDS) 100 102
39: 103 type=100 (BONDS) 102 103
39: 104 type=107 (BONDS) 102 104
39: 105 type=102 (BONDS) 104 105
39: 106 type=103 (BONDS) 104 106
39: 107 type=104 (BONDS) 104 115
39: 108 type=102 (BONDS) 106 107
39: 109 type=102 (BONDS) 106 108
39: 110 type=103 (BONDS) 106 109
39: 111 type=102 (BONDS) 109 110
39: 112 type=102 (BONDS) 109 111
39: 113 type=104 (BONDS) 109 112
39: 114 type=115 (BONDS) 112 113
39: 115 type=115 (BONDS) 112 114
39: 116 type=105 (BONDS) 115 116
39: 117 type=106 (BONDS) 115 117
39: 118 type=100 (BONDS) 117 118
39: 119 type=107 (BONDS) 117 119
39: 120 type=102 (BONDS) 119 120
39: 121 type=103 (BONDS) 119 121
39: 122 type=104 (BONDS) 119 134
39: 123 type=102 (BONDS) 121 122
39: 124 type=102 (BONDS) 121 123
39: 125 type=103 (BONDS) 121 124
39: 126 type=102 (BONDS) 124 125
39: 127 type=103 (BONDS) 124 126
39: 128 type=103 (BONDS) 124 130
39: 129 type=102 (BONDS) 126 127
39: 130 type=102 (BONDS) 126 128
39: 131 type=102 (BONDS) 126 129
39: 132 type=102 (BONDS) 130 131
39: 133 type=102 (BONDS) 130 132
39: 134 type=102 (BONDS) 130 133
39: 135 type=105 (BONDS) 134 135
39: 136 type=106 (BONDS) 134 136
39: 137 type=100 (BONDS) 136 137
39: 138 type=107 (BONDS) 136 138
39: 139 type=102 (BONDS) 138 139
39: 140 type=103 (BONDS) 138 140
39: 141 type=104 (BONDS) 138 144
39: 142 type=102 (BONDS) 140 141
39: 143 type=102 (BONDS) 140 142
39: 144 type=102 (BONDS) 140 143
39: 145 type=105 (BONDS) 144 145
39: 146 type=106 (BONDS) 144 146
39: 147 type=100 (BONDS) 146 147
39: 148 type=107 (BONDS) 146 148
39: 149 type=102 (BONDS) 148 149
39: 150 type=103 (BONDS) 148 150
39: 151 type=104 (BONDS) 148 154
39: 152 type=102 (BONDS) 150 151
39: 153 type=102 (BONDS) 150 152
39: 154 type=102 (BONDS) 150 153
39: 155 type=105 (BONDS) 154 155
39: G96Bond:
39: nr: 0
39: Morse:
39: nr: 0
39: Cubic Bonds:
39: nr: 0
39: Connect Bonds:
39: nr: 0
39: Harmonic Pot.:
39: nr: 0
39: FENE Bonds:
39: nr: 0
39: Tab. Bonds:
39: nr: 0
39: Tab. Bonds NC:
39: nr: 0
39: Restraint Pot.:
39: nr: 0
39: Angle:
39: nr: 1124
39: iatoms:
39: 0 type=116 (ANGLES) 1 0 2
39: 1 type=116 (ANGLES) 1 0 3
39: 2 type=116 (ANGLES) 1 0 4
39: 3 type=116 (ANGLES) 2 0 3
39: 4 type=116 (ANGLES) 2 0 4
39: 5 type=116 (ANGLES) 3 0 4
39: 6 type=116 (ANGLES) 0 4 5
39: 7 type=117 (ANGLES) 0 4 6
39: 8 type=117 (ANGLES) 0 4 22
39: 9 type=118 (ANGLES) 5 4 6
39: 10 type=116 (ANGLES) 5 4 22
39: 11 type=119 (ANGLES) 6 4 22
39: 12 type=118 (ANGLES) 4 6 7
39: 13 type=118 (ANGLES) 4 6 8
39: 14 type=120 (ANGLES) 4 6 9
39: 15 type=121 (ANGLES) 7 6 8
39: 16 type=118 (ANGLES) 7 6 9
39: 17 type=118 (ANGLES) 8 6 9
39: 18 type=118 (ANGLES) 6 9 10
39: 19 type=118 (ANGLES) 6 9 11
39: 20 type=120 (ANGLES) 6 9 12
39: 21 type=121 (ANGLES) 10 9 11
39: 22 type=118 (ANGLES) 10 9 12
39: 23 type=118 (ANGLES) 11 9 12
39: 24 type=118 (ANGLES) 9 12 13
39: 25 type=118 (ANGLES) 9 12 14
39: 26 type=120 (ANGLES) 9 12 15
39: 27 type=121 (ANGLES) 13 12 14
39: 28 type=118 (ANGLES) 13 12 15
39: 29 type=118 (ANGLES) 14 12 15
39: 30 type=118 (ANGLES) 12 15 16
39: 31 type=118 (ANGLES) 12 15 17
39: 32 type=117 (ANGLES) 12 15 18
39: 33 type=121 (ANGLES) 16 15 17
39: 34 type=116 (ANGLES) 16 15 18
39: 35 type=116 (ANGLES) 17 15 18
39: 36 type=116 (ANGLES) 15 18 19
39: 37 type=116 (ANGLES) 15 18 20
39: 38 type=116 (ANGLES) 15 18 21
39: 39 type=116 (ANGLES) 19 18 20
39: 40 type=116 (ANGLES) 19 18 21
39: 41 type=116 (ANGLES) 20 18 21
39: 42 type=122 (ANGLES) 4 22 23
39: 43 type=123 (ANGLES) 4 22 24
39: 44 type=124 (ANGLES) 23 22 24
39: 45 type=125 (ANGLES) 22 24 25
39: 46 type=126 (ANGLES) 22 24 26
39: 47 type=127 (ANGLES) 25 24 26
39: 48 type=116 (ANGLES) 24 26 27
39: 49 type=128 (ANGLES) 24 26 28
39: 50 type=129 (ANGLES) 24 26 38
39: 51 type=118 (ANGLES) 27 26 28
39: 52 type=116 (ANGLES) 27 26 38
39: 53 type=119 (ANGLES) 28 26 38
39: 54 type=118 (ANGLES) 26 28 29
39: 55 type=120 (ANGLES) 26 28 30
39: 56 type=120 (ANGLES) 26 28 34
39: 57 type=118 (ANGLES) 29 28 30
39: 58 type=118 (ANGLES) 29 28 34
39: 59 type=120 (ANGLES) 30 28 34
39: 60 type=118 (ANGLES) 28 30 31
39: 61 type=118 (ANGLES) 28 30 32
39: 62 type=118 (ANGLES) 28 30 33
39: 63 type=121 (ANGLES) 31 30 32
39: 64 type=121 (ANGLES) 31 30 33
39: 65 type=121 (ANGLES) 32 30 33
39: 66 type=118 (ANGLES) 28 34 35
39: 67 type=118 (ANGLES) 28 34 36
39: 68 type=118 (ANGLES) 28 34 37
39: 69 type=121 (ANGLES) 35 34 36
39: 70 type=121 (ANGLES) 35 34 37
39: 71 type=121 (ANGLES) 36 34 37
39: 72 type=122 (ANGLES) 26 38 39
39: 73 type=123 (ANGLES) 26 38 40
39: 74 type=124 (ANGLES) 39 38 40
39: 75 type=125 (ANGLES) 38 40 41
39: 76 type=126 (ANGLES) 38 40 42
39: 77 type=127 (ANGLES) 41 40 42
39: 78 type=116 (ANGLES) 40 42 43
39: 79 type=128 (ANGLES) 40 42 44
39: 80 type=129 (ANGLES) 40 42 58
39: 81 type=118 (ANGLES) 43 42 44
39: 82 type=116 (ANGLES) 43 42 58
39: 83 type=119 (ANGLES) 44 42 58
39: 84 type=118 (ANGLES) 42 44 45
39: 85 type=118 (ANGLES) 42 44 46
39: 86 type=130 (ANGLES) 42 44 47
39: 87 type=121 (ANGLES) 45 44 46
39: 88 type=116 (ANGLES) 45 44 47
39: 89 type=116 (ANGLES) 46 44 47
39: 90 type=131 (ANGLES) 44 47 48
39: 91 type=131 (ANGLES) 44 47 50
39: 92 type=132 (ANGLES) 48 47 50
39: 93 type=133 (ANGLES) 47 48 49
39: 94 type=132 (ANGLES) 47 48 52
39: 95 type=133 (ANGLES) 49 48 52
39: 96 type=133 (ANGLES) 47 50 51
39: 97 type=132 (ANGLES) 47 50 54
39: 98 type=133 (ANGLES) 51 50 54
39: 99 type=133 (ANGLES) 48 52 53
39: 100 type=132 (ANGLES) 48 52 56
39: 101 type=133 (ANGLES) 53 52 56
39: 102 type=133 (ANGLES) 50 54 55
39: 103 type=132 (ANGLES) 50 54 56
39: 104 type=133 (ANGLES) 55 54 56
39: 105 type=132 (ANGLES) 52 56 54
39: 106 type=133 (ANGLES) 52 56 57
39: 107 type=133 (ANGLES) 54 56 57
39: 108 type=122 (ANGLES) 42 58 59
39: 109 type=123 (ANGLES) 42 58 60
39: 110 type=124 (ANGLES) 59 58 60
39: 111 type=125 (ANGLES) 58 60 61
39: 112 type=126 (ANGLES) 58 60 62
39: 113 type=127 (ANGLES) 61 60 62
39: 114 type=116 (ANGLES) 60 62 63
39: 115 type=116 (ANGLES) 60 62 64
39: 116 type=129 (ANGLES) 60 62 65
39: 117 type=121 (ANGLES) 63 62 64
39: 118 type=116 (ANGLES) 63 62 65
39: 119 type=116 (ANGLES) 64 62 65
39: 120 type=122 (ANGLES) 62 65 66
39: 121 type=123 (ANGLES) 62 65 67
39: 122 type=124 (ANGLES) 66 65 67
39: 123 type=125 (ANGLES) 65 67 68
39: 124 type=126 (ANGLES) 65 67 69
39: 125 type=127 (ANGLES) 68 67 69
39: 126 type=116 (ANGLES) 67 69 70
39: 127 type=128 (ANGLES) 67 69 71
39: 128 type=129 (ANGLES) 67 69 89
39: 129 type=118 (ANGLES) 70 69 71
39: 130 type=116 (ANGLES) 70 69 89
39: 131 type=119 (ANGLES) 71 69 89
39: 132 type=118 (ANGLES) 69 71 72
39: 133 type=118 (ANGLES) 69 71 73
39: 134 type=120 (ANGLES) 69 71 74
39: 135 type=121 (ANGLES) 72 71 73
39: 136 type=118 (ANGLES) 72 71 74
39: 137 type=118 (ANGLES) 73 71 74
39: 138 type=118 (ANGLES) 71 74 75
39: 139 type=118 (ANGLES) 71 74 76
39: 140 type=120 (ANGLES) 71 74 77
39: 141 type=121 (ANGLES) 75 74 76
39: 142 type=118 (ANGLES) 75 74 77
39: 143 type=118 (ANGLES) 76 74 77
39: 144 type=118 (ANGLES) 74 77 78
39: 145 type=118 (ANGLES) 74 77 79
39: 146 type=117 (ANGLES) 74 77 80
39: 147 type=121 (ANGLES) 78 77 79
39: 148 type=116 (ANGLES) 78 77 80
39: 149 type=116 (ANGLES) 79 77 80
39: 150 type=134 (ANGLES) 77 80 81
39: 151 type=135 (ANGLES) 77 80 82
39: 152 type=133 (ANGLES) 81 80 82
39: 153 type=131 (ANGLES) 80 82 83
39: 154 type=131 (ANGLES) 80 82 86
39: 155 type=131 (ANGLES) 83 82 86
39: 156 type=133 (ANGLES) 82 83 84
39: 157 type=133 (ANGLES) 82 83 85
39: 158 type=133 (ANGLES) 84 83 85
39: 159 type=133 (ANGLES) 82 86 87
39: 160 type=133 (ANGLES) 82 86 88
39: 161 type=133 (ANGLES) 87 86 88
39: 162 type=122 (ANGLES) 69 89 90
39: 163 type=123 (ANGLES) 69 89 91
39: 164 type=124 (ANGLES) 90 89 91
39: 165 type=125 (ANGLES) 89 91 92
39: 166 type=126 (ANGLES) 89 91 93
39: 167 type=127 (ANGLES) 92 91 93
39: 168 type=116 (ANGLES) 91 93 94
39: 169 type=128 (ANGLES) 91 93 95
39: 170 type=129 (ANGLES) 91 93 100
39: 171 type=118 (ANGLES) 94 93 95
39: 172 type=116 (ANGLES) 94 93 100
39: 173 type=119 (ANGLES) 95 93 100
39: 174 type=118 (ANGLES) 93 95 96
39: 175 type=118 (ANGLES) 93 95 97
39: 176 type=136 (ANGLES) 93 95 98
39: 177 type=121 (ANGLES) 96 95 97
39: 178 type=116 (ANGLES) 96 95 98
39: 179 type=116 (ANGLES) 97 95 98
39: 180 type=137 (ANGLES) 95 98 99
39: 181 type=122 (ANGLES) 93 100 101
39: 182 type=123 (ANGLES) 93 100 102
39: 183 type=124 (ANGLES) 101 100 102
39: 184 type=125 (ANGLES) 100 102 103
39: 185 type=126 (ANGLES) 100 102 104
39: 186 type=127 (ANGLES) 103 102 104
39: 187 type=116 (ANGLES) 102 104 105
39: 188 type=128 (ANGLES) 102 104 106
39: 189 type=129 (ANGLES) 102 104 115
39: 190 type=118 (ANGLES) 105 104 106
39: 191 type=116 (ANGLES) 105 104 115
39: 192 type=119 (ANGLES) 106 104 115
39: 193 type=118 (ANGLES) 104 106 107
39: 194 type=118 (ANGLES) 104 106 108
39: 195 type=120 (ANGLES) 104 106 109
39: 196 type=121 (ANGLES) 107 106 108
39: 197 type=118 (ANGLES) 107 106 109
39: 198 type=118 (ANGLES) 108 106 109
39: 199 type=118 (ANGLES) 106 109 110
39: 200 type=118 (ANGLES) 106 109 111
39: 201 type=119 (ANGLES) 106 109 112
39: 202 type=121 (ANGLES) 110 109 111
39: 203 type=116 (ANGLES) 110 109 112
39: 204 type=116 (ANGLES) 111 109 112
39: 205 type=138 (ANGLES) 109 112 113
39: 206 type=138 (ANGLES) 109 112 114
39: 207 type=139 (ANGLES) 113 112 114
39: 208 type=122 (ANGLES) 104 115 116
39: 209 type=123 (ANGLES) 104 115 117
39: 210 type=124 (ANGLES) 116 115 117
39: 211 type=125 (ANGLES) 115 117 118
39: 212 type=126 (ANGLES) 115 117 119
39: 213 type=127 (ANGLES) 118 117 119
39: 214 type=116 (ANGLES) 117 119 120
39: 215 type=128 (ANGLES) 117 119 121
39: 216 type=129 (ANGLES) 117 119 134
39: 217 type=118 (ANGLES) 120 119 121
39: 218 type=116 (ANGLES) 120 119 134
39: 219 type=119 (ANGLES) 121 119 134
39: 220 type=118 (ANGLES) 119 121 122
39: 221 type=118 (ANGLES) 119 121 123
39: 222 type=120 (ANGLES) 119 121 124
39: 223 type=121 (ANGLES) 122 121 123
39: 224 type=118 (ANGLES) 122 121 124
39: 225 type=118 (ANGLES) 123 121 124
39: 226 type=118 (ANGLES) 121 124 125
39: 227 type=120 (ANGLES) 121 124 126
39: 228 type=120 (ANGLES) 121 124 130
39: 229 type=118 (ANGLES) 125 124 126
39: 230 type=118 (ANGLES) 125 124 130
39: 231 type=120 (ANGLES) 126 124 130
39: 232 type=118 (ANGLES) 124 126 127
39: 233 type=118 (ANGLES) 124 126 128
39: 234 type=118 (ANGLES) 124 126 129
39: 235 type=121 (ANGLES) 127 126 128
39: 236 type=121 (ANGLES) 127 126 129
39: 237 type=121 (ANGLES) 128 126 129
39: 238 type=118 (ANGLES) 124 130 131
39: 239 type=118 (ANGLES) 124 130 132
39: 240 type=118 (ANGLES) 124 130 133
39: 241 type=121 (ANGLES) 131 130 132
39: 242 type=121 (ANGLES) 131 130 133
39: 243 type=121 (ANGLES) 132 130 133
39: 244 type=122 (ANGLES) 119 134 135
39: 245 type=123 (ANGLES) 119 134 136
39: 246 type=124 (ANGLES) 135 134 136
39: 247 type=125 (ANGLES) 134 136 137
39: 248 type=126 (ANGLES) 134 136 138
39: 249 type=127 (ANGLES) 137 136 138
39: 250 type=116 (ANGLES) 136 138 139
39: 251 type=128 (ANGLES) 136 138 140
39: 252 type=129 (ANGLES) 136 138 144
39: 253 type=118 (ANGLES) 139 138 140
39: 254 type=116 (ANGLES) 139 138 144
39: 255 type=119 (ANGLES) 140 138 144
39: 256 type=118 (ANGLES) 138 140 141
39: 257 type=118 (ANGLES) 138 140 142
39: 258 type=118 (ANGLES) 138 140 143
39: 259 type=121 (ANGLES) 141 140 142
39: 260 type=121 (ANGLES) 141 140 143
39: 261 type=121 (ANGLES) 142 140 143
39: 262 type=122 (ANGLES) 138 144 145
39: 263 type=123 (ANGLES) 138 144 146
39: 264 type=124 (ANGLES) 145 144 146
39: 265 type=125 (ANGLES) 144 146 147
39: 266 type=126 (ANGLES) 144 146 148
39: 267 type=127 (ANGLES) 147 146 148
39: 268 type=116 (ANGLES) 146 148 149
39: 269 type=128 (ANGLES) 146 148 150
39: 270 type=129 (ANGLES) 146 148 154
39: 271 type=118 (ANGLES) 149 148 150
39: 272 type=116 (ANGLES) 149 148 154
39: 273 type=119 (ANGLES) 150 148 154
39: 274 type=118 (ANGLES) 148 150 151
39: 275 type=118 (ANGLES) 148 150 152
39: 276 type=118 (ANGLES) 148 150 153
39: 277 type=121 (ANGLES) 151 150 152
39: 278 type=121 (ANGLES) 151 150 153
39: 279 type=121 (ANGLES) 152 150 153
39: 280 type=122 (ANGLES) 148 154 155
39: G96Angle:
39: nr: 0
39: Restricted Angles:
39: nr: 0
39: Lin. Angle:
39: nr: 0
39: Bond-Cross:
39: nr: 0
39: BA-Cross:
39: nr: 0
39: U-B:
39: nr: 0
39: Quartic Angles:
39: nr: 0
39: Tab. Angles:
39: nr: 0
39: Proper Dih.:
39: nr: 145
39: iatoms:
39: 0 type=140 (PDIHS) 4 24 22 23
39: 1 type=141 (PDIHS) 22 26 24 25
39: 2 type=140 (PDIHS) 26 40 38 39
39: 3 type=141 (PDIHS) 38 42 40 41
39: 4 type=140 (PDIHS) 42 60 58 59
39: 5 type=142 (PDIHS) 44 47 50 48
39: 6 type=142 (PDIHS) 47 52 48 49
39: 7 type=142 (PDIHS) 47 54 50 51
39: 8 type=142 (PDIHS) 48 56 52 53
39: 9 type=142 (PDIHS) 50 56 54 55
39: 10 type=142 (PDIHS) 52 54 56 57
39: 11 type=141 (PDIHS) 58 62 60 61
39: 12 type=140 (PDIHS) 62 67 65 66
39: 13 type=141 (PDIHS) 65 69 67 68
39: 14 type=140 (PDIHS) 69 91 89 90
39: 15 type=141 (PDIHS) 77 82 80 81
39: 16 type=140 (PDIHS) 80 83 82 86
39: 17 type=141 (PDIHS) 82 84 83 85
39: 18 type=141 (PDIHS) 82 87 86 88
39: 19 type=141 (PDIHS) 89 93 91 92
39: 20 type=140 (PDIHS) 93 102 100 101
39: 21 type=141 (PDIHS) 100 104 102 103
39: 22 type=140 (PDIHS) 104 117 115 116
39: 23 type=140 (PDIHS) 109 113 112 114
39: 24 type=141 (PDIHS) 115 119 117 118
39: 25 type=140 (PDIHS) 119 136 134 135
39: 26 type=141 (PDIHS) 134 138 136 137
39: 27 type=140 (PDIHS) 138 146 144 145
39: 28 type=141 (PDIHS) 144 148 146 147
39: Ryckaert-Bell.:
39: nr: 1565
39: iatoms:
39: 0 type=143 (RBDIHS) 1 0 4 5
39: 1 type=144 (RBDIHS) 1 0 4 6
39: 2 type=144 (RBDIHS) 1 0 4 22
39: 3 type=143 (RBDIHS) 2 0 4 5
39: 4 type=144 (RBDIHS) 2 0 4 6
39: 5 type=144 (RBDIHS) 2 0 4 22
39: 6 type=143 (RBDIHS) 3 0 4 5
39: 7 type=144 (RBDIHS) 3 0 4 6
39: 8 type=144 (RBDIHS) 3 0 4 22
39: 9 type=145 (RBDIHS) 0 4 6 9
39: 10 type=146 (RBDIHS) 22 4 6 9
39: 11 type=147 (RBDIHS) 0 4 6 7
39: 12 type=147 (RBDIHS) 0 4 6 8
39: 13 type=148 (RBDIHS) 5 4 6 7
39: 14 type=148 (RBDIHS) 5 4 6 8
39: 15 type=148 (RBDIHS) 5 4 6 9
39: 16 type=149 (RBDIHS) 22 4 6 7
39: 17 type=149 (RBDIHS) 22 4 6 8
39: 18 type=150 (RBDIHS) 0 4 22 24
39: 19 type=151 (RBDIHS) 6 4 22 24
39: 20 type=148 (RBDIHS) 4 6 9 10
39: 21 type=148 (RBDIHS) 4 6 9 11
39: 22 type=152 (RBDIHS) 4 6 9 12
39: 23 type=148 (RBDIHS) 7 6 9 10
39: 24 type=148 (RBDIHS) 7 6 9 11
39: 25 type=148 (RBDIHS) 7 6 9 12
39: 26 type=148 (RBDIHS) 8 6 9 10
39: 27 type=148 (RBDIHS) 8 6 9 11
39: 28 type=148 (RBDIHS) 8 6 9 12
39: 29 type=148 (RBDIHS) 6 9 12 13
39: 30 type=148 (RBDIHS) 6 9 12 14
39: 31 type=152 (RBDIHS) 6 9 12 15
39: 32 type=148 (RBDIHS) 10 9 12 13
39: 33 type=148 (RBDIHS) 10 9 12 14
39: 34 type=148 (RBDIHS) 10 9 12 15
39: 35 type=148 (RBDIHS) 11 9 12 13
39: 36 type=148 (RBDIHS) 11 9 12 14
39: 37 type=148 (RBDIHS) 11 9 12 15
39: 38 type=148 (RBDIHS) 9 12 15 16
39: 39 type=148 (RBDIHS) 9 12 15 17
39: 40 type=153 (RBDIHS) 9 12 15 18
39: 41 type=148 (RBDIHS) 13 12 15 16
39: 42 type=148 (RBDIHS) 13 12 15 17
39: 43 type=154 (RBDIHS) 13 12 15 18
39: 44 type=148 (RBDIHS) 14 12 15 16
39: 45 type=148 (RBDIHS) 14 12 15 17
39: 46 type=154 (RBDIHS) 14 12 15 18
39: 47 type=144 (RBDIHS) 12 15 18 19
39: 48 type=144 (RBDIHS) 12 15 18 20
39: 49 type=144 (RBDIHS) 12 15 18 21
39: 50 type=143 (RBDIHS) 16 15 18 19
39: 51 type=143 (RBDIHS) 16 15 18 20
39: 52 type=143 (RBDIHS) 16 15 18 21
39: 53 type=143 (RBDIHS) 17 15 18 19
39: 54 type=143 (RBDIHS) 17 15 18 20
39: 55 type=143 (RBDIHS) 17 15 18 21
39: 56 type=155 (RBDIHS) 4 22 24 25
39: 57 type=156 (RBDIHS) 4 22 24 26
39: 58 type=155 (RBDIHS) 23 22 24 25
39: 59 type=157 (RBDIHS) 23 22 24 26
39: 60 type=158 (RBDIHS) 22 24 26 28
39: 61 type=159 (RBDIHS) 22 24 26 38
39: 62 type=160 (RBDIHS) 24 26 28 30
39: 63 type=160 (RBDIHS) 24 26 28 34
39: 64 type=161 (RBDIHS) 38 26 28 30
39: 65 type=161 (RBDIHS) 38 26 28 34
39: 66 type=147 (RBDIHS) 24 26 28 29
39: 67 type=148 (RBDIHS) 27 26 28 29
39: 68 type=148 (RBDIHS) 27 26 28 30
39: 69 type=148 (RBDIHS) 27 26 28 34
39: 70 type=149 (RBDIHS) 38 26 28 29
39: 71 type=150 (RBDIHS) 24 26 38 40
39: 72 type=151 (RBDIHS) 28 26 38 40
39: 73 type=148 (RBDIHS) 26 28 30 31
39: 74 type=148 (RBDIHS) 26 28 30 32
39: 75 type=148 (RBDIHS) 26 28 30 33
39: 76 type=148 (RBDIHS) 29 28 30 31
39: 77 type=148 (RBDIHS) 29 28 30 32
39: 78 type=148 (RBDIHS) 29 28 30 33
39: 79 type=148 (RBDIHS) 34 28 30 31
39: 80 type=148 (RBDIHS) 34 28 30 32
39: 81 type=148 (RBDIHS) 34 28 30 33
39: 82 type=148 (RBDIHS) 26 28 34 35
39: 83 type=148 (RBDIHS) 26 28 34 36
39: 84 type=148 (RBDIHS) 26 28 34 37
39: 85 type=148 (RBDIHS) 29 28 34 35
39: 86 type=148 (RBDIHS) 29 28 34 36
39: 87 type=148 (RBDIHS) 29 28 34 37
39: 88 type=148 (RBDIHS) 30 28 34 35
39: 89 type=148 (RBDIHS) 30 28 34 36
39: 90 type=148 (RBDIHS) 30 28 34 37
39: 91 type=155 (RBDIHS) 26 38 40 41
39: 92 type=156 (RBDIHS) 26 38 40 42
39: 93 type=155 (RBDIHS) 39 38 40 41
39: 94 type=157 (RBDIHS) 39 38 40 42
39: 95 type=158 (RBDIHS) 38 40 42 44
39: 96 type=159 (RBDIHS) 38 40 42 58
39: 97 type=147 (RBDIHS) 40 42 44 45
39: 98 type=147 (RBDIHS) 40 42 44 46
39: 99 type=162 (RBDIHS) 40 42 44 47
39: 100 type=148 (RBDIHS) 43 42 44 45
39: 101 type=148 (RBDIHS) 43 42 44 46
39: 102 type=163 (RBDIHS) 43 42 44 47
39: 103 type=149 (RBDIHS) 58 42 44 45
39: 104 type=149 (RBDIHS) 58 42 44 46
39: 105 type=164 (RBDIHS) 58 42 44 47
39: 106 type=150 (RBDIHS) 40 42 58 60
39: 107 type=151 (RBDIHS) 44 42 58 60
39: 108 type=165 (RBDIHS) 44 47 48 49
39: 109 type=165 (RBDIHS) 44 47 48 52
39: 110 type=165 (RBDIHS) 50 47 48 49
39: 111 type=165 (RBDIHS) 50 47 48 52
39: 112 type=165 (RBDIHS) 44 47 50 51
39: 113 type=165 (RBDIHS) 44 47 50 54
39: 114 type=165 (RBDIHS) 48 47 50 51
39: 115 type=165 (RBDIHS) 48 47 50 54
39: 116 type=165 (RBDIHS) 47 48 52 53
39: 117 type=165 (RBDIHS) 47 48 52 56
39: 118 type=165 (RBDIHS) 49 48 52 53
39: 119 type=165 (RBDIHS) 49 48 52 56
39: 120 type=165 (RBDIHS) 47 50 54 55
39: 121 type=165 (RBDIHS) 47 50 54 56
39: 122 type=165 (RBDIHS) 51 50 54 55
39: 123 type=165 (RBDIHS) 51 50 54 56
39: 124 type=165 (RBDIHS) 48 52 56 54
39: 125 type=165 (RBDIHS) 48 52 56 57
39: 126 type=165 (RBDIHS) 53 52 56 54
39: 127 type=165 (RBDIHS) 53 52 56 57
39: 128 type=165 (RBDIHS) 50 54 56 52
39: 129 type=165 (RBDIHS) 50 54 56 57
39: 130 type=165 (RBDIHS) 55 54 56 52
39: 131 type=165 (RBDIHS) 55 54 56 57
39: 132 type=155 (RBDIHS) 42 58 60 61
39: 133 type=156 (RBDIHS) 42 58 60 62
39: 134 type=155 (RBDIHS) 59 58 60 61
39: 135 type=157 (RBDIHS) 59 58 60 62
39: 136 type=159 (RBDIHS) 58 60 62 65
39: 137 type=150 (RBDIHS) 60 62 65 67
39: 138 type=155 (RBDIHS) 62 65 67 68
39: 139 type=156 (RBDIHS) 62 65 67 69
39: 140 type=155 (RBDIHS) 66 65 67 68
39: 141 type=157 (RBDIHS) 66 65 67 69
39: 142 type=158 (RBDIHS) 65 67 69 71
39: 143 type=159 (RBDIHS) 65 67 69 89
39: 144 type=166 (RBDIHS) 67 69 71 74
39: 145 type=167 (RBDIHS) 89 69 71 74
39: 146 type=147 (RBDIHS) 67 69 71 72
39: 147 type=147 (RBDIHS) 67 69 71 73
39: 148 type=148 (RBDIHS) 70 69 71 72
39: 149 type=148 (RBDIHS) 70 69 71 73
39: 150 type=148 (RBDIHS) 70 69 71 74
39: 151 type=149 (RBDIHS) 89 69 71 72
39: 152 type=149 (RBDIHS) 89 69 71 73
39: 153 type=150 (RBDIHS) 67 69 89 91
39: 154 type=151 (RBDIHS) 71 69 89 91
39: 155 type=148 (RBDIHS) 69 71 74 75
39: 156 type=148 (RBDIHS) 69 71 74 76
39: 157 type=152 (RBDIHS) 69 71 74 77
39: 158 type=148 (RBDIHS) 72 71 74 75
39: 159 type=148 (RBDIHS) 72 71 74 76
39: 160 type=148 (RBDIHS) 72 71 74 77
39: 161 type=148 (RBDIHS) 73 71 74 75
39: 162 type=148 (RBDIHS) 73 71 74 76
39: 163 type=148 (RBDIHS) 73 71 74 77
39: 164 type=148 (RBDIHS) 71 74 77 78
39: 165 type=148 (RBDIHS) 71 74 77 79
39: 166 type=153 (RBDIHS) 71 74 77 80
39: 167 type=148 (RBDIHS) 75 74 77 78
39: 168 type=148 (RBDIHS) 75 74 77 79
39: 169 type=168 (RBDIHS) 75 74 77 80
39: 170 type=148 (RBDIHS) 76 74 77 78
39: 171 type=148 (RBDIHS) 76 74 77 79
39: 172 type=168 (RBDIHS) 76 74 77 80
39: 173 type=169 (RBDIHS) 74 77 80 81
39: 174 type=170 (RBDIHS) 74 77 80 82
39: 175 type=171 (RBDIHS) 78 77 80 82
39: 176 type=171 (RBDIHS) 79 77 80 82
39: 177 type=172 (RBDIHS) 77 80 82 83
39: 178 type=172 (RBDIHS) 77 80 82 86
39: 179 type=173 (RBDIHS) 81 80 82 83
39: 180 type=173 (RBDIHS) 81 80 82 86
39: 181 type=173 (RBDIHS) 80 82 83 84
39: 182 type=173 (RBDIHS) 80 82 83 85
39: 183 type=173 (RBDIHS) 86 82 83 84
39: 184 type=173 (RBDIHS) 86 82 83 85
39: 185 type=173 (RBDIHS) 80 82 86 87
39: 186 type=173 (RBDIHS) 80 82 86 88
39: 187 type=173 (RBDIHS) 83 82 86 87
39: 188 type=173 (RBDIHS) 83 82 86 88
39: 189 type=155 (RBDIHS) 69 89 91 92
39: 190 type=156 (RBDIHS) 69 89 91 93
39: 191 type=155 (RBDIHS) 90 89 91 92
39: 192 type=157 (RBDIHS) 90 89 91 93
39: 193 type=158 (RBDIHS) 89 91 93 95
39: 194 type=159 (RBDIHS) 89 91 93 100
39: 195 type=174 (RBDIHS) 91 93 95 98
39: 196 type=175 (RBDIHS) 100 93 95 98
39: 197 type=147 (RBDIHS) 91 93 95 96
39: 198 type=147 (RBDIHS) 91 93 95 97
39: 199 type=148 (RBDIHS) 94 93 95 96
39: 200 type=148 (RBDIHS) 94 93 95 97
39: 201 type=176 (RBDIHS) 94 93 95 98
39: 202 type=149 (RBDIHS) 100 93 95 96
39: 203 type=149 (RBDIHS) 100 93 95 97
39: 204 type=150 (RBDIHS) 91 93 100 102
39: 205 type=151 (RBDIHS) 95 93 100 102
39: 206 type=177 (RBDIHS) 93 95 98 99
39: 207 type=178 (RBDIHS) 96 95 98 99
39: 208 type=178 (RBDIHS) 97 95 98 99
39: 209 type=155 (RBDIHS) 93 100 102 103
39: 210 type=156 (RBDIHS) 93 100 102 104
39: 211 type=155 (RBDIHS) 101 100 102 103
39: 212 type=157 (RBDIHS) 101 100 102 104
39: 213 type=158 (RBDIHS) 100 102 104 106
39: 214 type=159 (RBDIHS) 100 102 104 115
39: 215 type=179 (RBDIHS) 102 104 106 109
39: 216 type=180 (RBDIHS) 115 104 106 109
39: 217 type=147 (RBDIHS) 102 104 106 107
39: 218 type=147 (RBDIHS) 102 104 106 108
39: 219 type=148 (RBDIHS) 105 104 106 107
39: 220 type=148 (RBDIHS) 105 104 106 108
39: 221 type=148 (RBDIHS) 105 104 106 109
39: 222 type=149 (RBDIHS) 115 104 106 107
39: 223 type=149 (RBDIHS) 115 104 106 108
39: 224 type=150 (RBDIHS) 102 104 115 117
39: 225 type=151 (RBDIHS) 106 104 115 117
39: 226 type=148 (RBDIHS) 104 106 109 110
39: 227 type=148 (RBDIHS) 104 106 109 111
39: 228 type=181 (RBDIHS) 104 106 109 112
39: 229 type=148 (RBDIHS) 107 106 109 110
39: 230 type=148 (RBDIHS) 107 106 109 111
39: 231 type=182 (RBDIHS) 107 106 109 112
39: 232 type=148 (RBDIHS) 108 106 109 110
39: 233 type=148 (RBDIHS) 108 106 109 111
39: 234 type=182 (RBDIHS) 108 106 109 112
39: 235 type=183 (RBDIHS) 106 109 112 113
39: 236 type=183 (RBDIHS) 106 109 112 114
39: 237 type=155 (RBDIHS) 104 115 117 118
39: 238 type=156 (RBDIHS) 104 115 117 119
39: 239 type=155 (RBDIHS) 116 115 117 118
39: 240 type=157 (RBDIHS) 116 115 117 119
39: 241 type=158 (RBDIHS) 115 117 119 121
39: 242 type=159 (RBDIHS) 115 117 119 134
39: 243 type=184 (RBDIHS) 117 119 121 124
39: 244 type=185 (RBDIHS) 134 119 121 124
39: 245 type=147 (RBDIHS) 117 119 121 122
39: 246 type=147 (RBDIHS) 117 119 121 123
39: 247 type=148 (RBDIHS) 120 119 121 122
39: 248 type=148 (RBDIHS) 120 119 121 123
39: 249 type=148 (RBDIHS) 120 119 121 124
39: 250 type=149 (RBDIHS) 134 119 121 122
39: 251 type=149 (RBDIHS) 134 119 121 123
39: 252 type=150 (RBDIHS) 117 119 134 136
39: 253 type=151 (RBDIHS) 121 119 134 136
39: 254 type=148 (RBDIHS) 119 121 124 125
39: 255 type=152 (RBDIHS) 119 121 124 126
39: 256 type=152 (RBDIHS) 119 121 124 130
39: 257 type=148 (RBDIHS) 122 121 124 125
39: 258 type=148 (RBDIHS) 122 121 124 126
39: 259 type=148 (RBDIHS) 122 121 124 130
39: 260 type=148 (RBDIHS) 123 121 124 125
39: 261 type=148 (RBDIHS) 123 121 124 126
39: 262 type=148 (RBDIHS) 123 121 124 130
39: 263 type=148 (RBDIHS) 121 124 126 127
39: 264 type=148 (RBDIHS) 121 124 126 128
39: 265 type=148 (RBDIHS) 121 124 126 129
39: 266 type=148 (RBDIHS) 125 124 126 127
39: 267 type=148 (RBDIHS) 125 124 126 128
39: 268 type=148 (RBDIHS) 125 124 126 129
39: 269 type=148 (RBDIHS) 130 124 126 127
39: 270 type=148 (RBDIHS) 130 124 126 128
39: 271 type=148 (RBDIHS) 130 124 126 129
39: 272 type=148 (RBDIHS) 121 124 130 131
39: 273 type=148 (RBDIHS) 121 124 130 132
39: 274 type=148 (RBDIHS) 121 124 130 133
39: 275 type=148 (RBDIHS) 125 124 130 131
39: 276 type=148 (RBDIHS) 125 124 130 132
39: 277 type=148 (RBDIHS) 125 124 130 133
39: 278 type=148 (RBDIHS) 126 124 130 131
39: 279 type=148 (RBDIHS) 126 124 130 132
39: 280 type=148 (RBDIHS) 126 124 130 133
39: 281 type=155 (RBDIHS) 119 134 136 137
39: 282 type=156 (RBDIHS) 119 134 136 138
39: 283 type=155 (RBDIHS) 135 134 136 137
39: 284 type=157 (RBDIHS) 135 134 136 138
39: 285 type=158 (RBDIHS) 134 136 138 140
39: 286 type=159 (RBDIHS) 134 136 138 144
39: 287 type=147 (RBDIHS) 136 138 140 141
39: 288 type=147 (RBDIHS) 136 138 140 142
39: 289 type=147 (RBDIHS) 136 138 140 143
39: 290 type=148 (RBDIHS) 139 138 140 141
39: 291 type=148 (RBDIHS) 139 138 140 142
39: 292 type=148 (RBDIHS) 139 138 140 143
39: 293 type=149 (RBDIHS) 144 138 140 141
39: 294 type=149 (RBDIHS) 144 138 140 142
39: 295 type=149 (RBDIHS) 144 138 140 143
39: 296 type=150 (RBDIHS) 136 138 144 146
39: 297 type=151 (RBDIHS) 140 138 144 146
39: 298 type=155 (RBDIHS) 138 144 146 147
39: 299 type=156 (RBDIHS) 138 144 146 148
39: 300 type=155 (RBDIHS) 145 144 146 147
39: 301 type=157 (RBDIHS) 145 144 146 148
39: 302 type=158 (RBDIHS) 144 146 148 150
39: 303 type=159 (RBDIHS) 144 146 148 154
39: 304 type=147 (RBDIHS) 146 148 150 151
39: 305 type=147 (RBDIHS) 146 148 150 152
39: 306 type=147 (RBDIHS) 146 148 150 153
39: 307 type=148 (RBDIHS) 149 148 150 151
39: 308 type=148 (RBDIHS) 149 148 150 152
39: 309 type=148 (RBDIHS) 149 148 150 153
39: 310 type=149 (RBDIHS) 154 148 150 151
39: 311 type=149 (RBDIHS) 154 148 150 152
39: 312 type=149 (RBDIHS) 154 148 150 153
39: Restricted Dih.:
39: nr: 0
39: CBT Dih.:
39: nr: 0
39: Fourier Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Tab. Dih.:
39: nr: 0
39: CMAP Dih.:
39: nr: 0
39: GB 1-2 Pol. (unused):
39: nr: 0
39: GB 1-3 Pol. (unused):
39: nr: 0
39: GB 1-4 Pol. (unused):
39: nr: 0
39: GB Polarization (unused):
39: nr: 0
39: Nonpolar Sol. (unused):
39: nr: 0
39: LJ-14:
39: nr: 1197
39: iatoms:
39: 0 type=186 (LJ14) 0 7
39: 1 type=186 (LJ14) 0 8
39: 2 type=187 (LJ14) 0 9
39: 3 type=188 (LJ14) 0 23
39: 4 type=189 (LJ14) 0 24
39: 5 type=190 (LJ14) 1 5
39: 6 type=190 (LJ14) 1 6
39: 7 type=190 (LJ14) 1 22
39: 8 type=190 (LJ14) 2 5
39: 9 type=190 (LJ14) 2 6
39: 10 type=190 (LJ14) 2 22
39: 11 type=190 (LJ14) 3 5
39: 12 type=190 (LJ14) 3 6
39: 13 type=190 (LJ14) 3 22
39: 14 type=191 (LJ14) 4 10
39: 15 type=191 (LJ14) 4 11
39: 16 type=192 (LJ14) 4 12
39: 17 type=190 (LJ14) 4 25
39: 18 type=192 (LJ14) 4 26
39: 19 type=193 (LJ14) 5 7
39: 20 type=193 (LJ14) 5 8
39: 21 type=191 (LJ14) 5 9
39: 22 type=194 (LJ14) 5 23
39: 23 type=186 (LJ14) 5 24
39: 24 type=191 (LJ14) 6 13
39: 25 type=191 (LJ14) 6 14
39: 26 type=192 (LJ14) 6 15
39: 27 type=195 (LJ14) 6 23
39: 28 type=187 (LJ14) 6 24
39: 29 type=193 (LJ14) 7 10
39: 30 type=193 (LJ14) 7 11
39: 31 type=191 (LJ14) 7 12
39: 32 type=196 (LJ14) 7 22
39: 33 type=193 (LJ14) 8 10
39: 34 type=193 (LJ14) 8 11
39: 35 type=191 (LJ14) 8 12
39: 36 type=196 (LJ14) 8 22
39: 37 type=191 (LJ14) 9 16
39: 38 type=191 (LJ14) 9 17
39: 39 type=187 (LJ14) 9 18
39: 40 type=197 (LJ14) 9 22
39: 41 type=193 (LJ14) 10 13
39: 42 type=193 (LJ14) 10 14
39: 43 type=191 (LJ14) 10 15
39: 44 type=193 (LJ14) 11 13
39: 45 type=193 (LJ14) 11 14
39: 46 type=191 (LJ14) 11 15
39: 47 type=190 (LJ14) 12 19
39: 48 type=190 (LJ14) 12 20
39: 49 type=190 (LJ14) 12 21
39: 50 type=193 (LJ14) 13 16
39: 51 type=193 (LJ14) 13 17
39: 52 type=186 (LJ14) 13 18
39: 53 type=193 (LJ14) 14 16
39: 54 type=193 (LJ14) 14 17
39: 55 type=186 (LJ14) 14 18
39: 56 type=190 (LJ14) 16 19
39: 57 type=190 (LJ14) 16 20
39: 58 type=190 (LJ14) 16 21
39: 59 type=190 (LJ14) 17 19
39: 60 type=190 (LJ14) 17 20
39: 61 type=190 (LJ14) 17 21
39: 62 type=196 (LJ14) 22 27
39: 63 type=197 (LJ14) 22 28
39: 64 type=198 (LJ14) 22 38
39: 65 type=190 (LJ14) 23 25
39: 66 type=195 (LJ14) 23 26
39: 67 type=186 (LJ14) 24 29
39: 68 type=187 (LJ14) 24 30
39: 69 type=187 (LJ14) 24 34
39: 70 type=188 (LJ14) 24 39
39: 71 type=189 (LJ14) 24 40
39: 72 type=190 (LJ14) 25 27
39: 73 type=190 (LJ14) 25 28
39: 74 type=190 (LJ14) 25 38
39: 75 type=191 (LJ14) 26 31
39: 76 type=191 (LJ14) 26 32
39: 77 type=191 (LJ14) 26 33
39: 78 type=191 (LJ14) 26 35
39: 79 type=191 (LJ14) 26 36
39: 80 type=191 (LJ14) 26 37
39: 81 type=190 (LJ14) 26 41
39: 82 type=192 (LJ14) 26 42
39: 83 type=193 (LJ14) 27 29
39: 84 type=191 (LJ14) 27 30
39: 85 type=191 (LJ14) 27 34
39: 86 type=194 (LJ14) 27 39
39: 87 type=186 (LJ14) 27 40
39: 88 type=195 (LJ14) 28 39
39: 89 type=187 (LJ14) 28 40
39: 90 type=193 (LJ14) 29 31
39: 91 type=193 (LJ14) 29 32
39: 92 type=193 (LJ14) 29 33
39: 93 type=193 (LJ14) 29 35
39: 94 type=193 (LJ14) 29 36
39: 95 type=193 (LJ14) 29 37
39: 96 type=196 (LJ14) 29 38
39: 97 type=191 (LJ14) 30 35
39: 98 type=191 (LJ14) 30 36
39: 99 type=191 (LJ14) 30 37
39: 100 type=197 (LJ14) 30 38
39: 101 type=191 (LJ14) 31 34
39: 102 type=191 (LJ14) 32 34
39: 103 type=191 (LJ14) 33 34
39: 104 type=197 (LJ14) 34 38
39: 105 type=196 (LJ14) 38 43
39: 106 type=197 (LJ14) 38 44
39: 107 type=198 (LJ14) 38 58
39: 108 type=190 (LJ14) 39 41
39: 109 type=195 (LJ14) 39 42
39: 110 type=186 (LJ14) 40 45
39: 111 type=186 (LJ14) 40 46
39: 112 type=199 (LJ14) 40 47
39: 113 type=188 (LJ14) 40 59
39: 114 type=189 (LJ14) 40 60
39: 115 type=190 (LJ14) 41 43
39: 116 type=190 (LJ14) 41 44
39: 117 type=190 (LJ14) 41 58
39: 118 type=200 (LJ14) 42 48
39: 119 type=200 (LJ14) 42 50
39: 120 type=190 (LJ14) 42 61
39: 121 type=192 (LJ14) 42 62
39: 122 type=193 (LJ14) 43 45
39: 123 type=193 (LJ14) 43 46
39: 124 type=201 (LJ14) 43 47
39: 125 type=194 (LJ14) 43 59
39: 126 type=186 (LJ14) 43 60
39: 127 type=202 (LJ14) 44 49
39: 128 type=202 (LJ14) 44 51
39: 129 type=200 (LJ14) 44 52
39: 130 type=200 (LJ14) 44 54
39: 131 type=195 (LJ14) 44 59
39: 132 type=187 (LJ14) 44 60
39: 133 type=201 (LJ14) 45 48
39: 134 type=201 (LJ14) 45 50
39: 135 type=196 (LJ14) 45 58
39: 136 type=201 (LJ14) 46 48
39: 137 type=201 (LJ14) 46 50
39: 138 type=196 (LJ14) 46 58
39: 139 type=203 (LJ14) 47 53
39: 140 type=203 (LJ14) 47 55
39: 141 type=204 (LJ14) 47 56
39: 142 type=205 (LJ14) 47 58
39: 143 type=203 (LJ14) 48 51
39: 144 type=204 (LJ14) 48 54
39: 145 type=203 (LJ14) 48 57
39: 146 type=203 (LJ14) 49 50
39: 147 type=206 (LJ14) 49 53
39: 148 type=203 (LJ14) 49 56
39: 149 type=204 (LJ14) 50 52
39: 150 type=203 (LJ14) 50 57
39: 151 type=206 (LJ14) 51 55
39: 152 type=203 (LJ14) 51 56
39: 153 type=203 (LJ14) 52 55
39: 154 type=203 (LJ14) 53 54
39: 155 type=206 (LJ14) 53 57
39: 156 type=206 (LJ14) 55 57
39: 157 type=196 (LJ14) 58 63
39: 158 type=196 (LJ14) 58 64
39: 159 type=198 (LJ14) 58 65
39: 160 type=190 (LJ14) 59 61
39: 161 type=195 (LJ14) 59 62
39: 162 type=188 (LJ14) 60 66
39: 163 type=189 (LJ14) 60 67
39: 164 type=190 (LJ14) 61 63
39: 165 type=190 (LJ14) 61 64
39: 166 type=190 (LJ14) 61 65
39: 167 type=190 (LJ14) 62 68
39: 168 type=192 (LJ14) 62 69
39: 169 type=194 (LJ14) 63 66
39: 170 type=186 (LJ14) 63 67
39: 171 type=194 (LJ14) 64 66
39: 172 type=186 (LJ14) 64 67
39: 173 type=196 (LJ14) 65 70
39: 174 type=197 (LJ14) 65 71
39: 175 type=198 (LJ14) 65 89
39: 176 type=190 (LJ14) 66 68
39: 177 type=195 (LJ14) 66 69
39: 178 type=186 (LJ14) 67 72
39: 179 type=186 (LJ14) 67 73
39: 180 type=187 (LJ14) 67 74
39: 181 type=188 (LJ14) 67 90
39: 182 type=189 (LJ14) 67 91
39: 183 type=190 (LJ14) 68 70
39: 184 type=190 (LJ14) 68 71
39: 185 type=190 (LJ14) 68 89
39: 186 type=191 (LJ14) 69 75
39: 187 type=191 (LJ14) 69 76
39: 188 type=192 (LJ14) 69 77
39: 189 type=190 (LJ14) 69 92
39: 190 type=192 (LJ14) 69 93
39: 191 type=193 (LJ14) 70 72
39: 192 type=193 (LJ14) 70 73
39: 193 type=191 (LJ14) 70 74
39: 194 type=194 (LJ14) 70 90
39: 195 type=186 (LJ14) 70 91
39: 196 type=191 (LJ14) 71 78
39: 197 type=191 (LJ14) 71 79
39: 198 type=187 (LJ14) 71 80
39: 199 type=195 (LJ14) 71 90
39: 200 type=187 (LJ14) 71 91
39: 201 type=193 (LJ14) 72 75
39: 202 type=193 (LJ14) 72 76
39: 203 type=191 (LJ14) 72 77
39: 204 type=196 (LJ14) 72 89
39: 205 type=193 (LJ14) 73 75
39: 206 type=193 (LJ14) 73 76
39: 207 type=191 (LJ14) 73 77
39: 208 type=196 (LJ14) 73 89
39: 209 type=190 (LJ14) 74 81
39: 210 type=207 (LJ14) 74 82
39: 211 type=197 (LJ14) 74 89
39: 212 type=193 (LJ14) 75 78
39: 213 type=193 (LJ14) 75 79
39: 214 type=186 (LJ14) 75 80
39: 215 type=193 (LJ14) 76 78
39: 216 type=193 (LJ14) 76 79
39: 217 type=186 (LJ14) 76 80
39: 218 type=187 (LJ14) 77 83
39: 219 type=187 (LJ14) 77 86
39: 220 type=190 (LJ14) 78 81
39: 221 type=208 (LJ14) 78 82
39: 222 type=190 (LJ14) 79 81
39: 223 type=208 (LJ14) 79 82
39: 224 type=190 (LJ14) 80 84
39: 225 type=190 (LJ14) 80 85
39: 226 type=190 (LJ14) 80 87
39: 227 type=190 (LJ14) 80 88
39: 228 type=190 (LJ14) 81 83
39: 229 type=190 (LJ14) 81 86
39: 230 type=190 (LJ14) 83 87
39: 231 type=190 (LJ14) 83 88
39: 232 type=190 (LJ14) 84 86
39: 233 type=190 (LJ14) 85 86
39: 234 type=196 (LJ14) 89 94
39: 235 type=197 (LJ14) 89 95
39: 236 type=198 (LJ14) 89 100
39: 237 type=190 (LJ14) 90 92
39: 238 type=195 (LJ14) 90 93
39: 239 type=186 (LJ14) 91 96
39: 240 type=186 (LJ14) 91 97
39: 241 type=209 (LJ14) 91 98
39: 242 type=188 (LJ14) 91 101
39: 243 type=189 (LJ14) 91 102
39: 244 type=190 (LJ14) 92 94
39: 245 type=190 (LJ14) 92 95
39: 246 type=190 (LJ14) 92 100
39: 247 type=190 (LJ14) 93 99
39: 248 type=190 (LJ14) 93 103
39: 249 type=192 (LJ14) 93 104
39: 250 type=193 (LJ14) 94 96
39: 251 type=193 (LJ14) 94 97
39: 252 type=210 (LJ14) 94 98
39: 253 type=194 (LJ14) 94 101
39: 254 type=186 (LJ14) 94 102
39: 255 type=195 (LJ14) 95 101
39: 256 type=187 (LJ14) 95 102
39: 257 type=190 (LJ14) 96 99
39: 258 type=196 (LJ14) 96 100
39: 259 type=190 (LJ14) 97 99
39: 260 type=196 (LJ14) 97 100
39: 261 type=211 (LJ14) 98 100
39: 262 type=196 (LJ14) 100 105
39: 263 type=197 (LJ14) 100 106
39: 264 type=198 (LJ14) 100 115
39: 265 type=190 (LJ14) 101 103
39: 266 type=195 (LJ14) 101 104
39: 267 type=186 (LJ14) 102 107
39: 268 type=186 (LJ14) 102 108
39: 269 type=187 (LJ14) 102 109
39: 270 type=188 (LJ14) 102 116
39: 271 type=189 (LJ14) 102 117
39: 272 type=190 (LJ14) 103 105
39: 273 type=190 (LJ14) 103 106
39: 274 type=190 (LJ14) 103 115
39: 275 type=191 (LJ14) 104 110
39: 276 type=191 (LJ14) 104 111
39: 277 type=197 (LJ14) 104 112
39: 278 type=190 (LJ14) 104 118
39: 279 type=192 (LJ14) 104 119
39: 280 type=193 (LJ14) 105 107
39: 281 type=193 (LJ14) 105 108
39: 282 type=191 (LJ14) 105 109
39: 283 type=194 (LJ14) 105 116
39: 284 type=186 (LJ14) 105 117
39: 285 type=195 (LJ14) 106 113
39: 286 type=195 (LJ14) 106 114
39: 287 type=195 (LJ14) 106 116
39: 288 type=187 (LJ14) 106 117
39: 289 type=193 (LJ14) 107 110
39: 290 type=193 (LJ14) 107 111
39: 291 type=196 (LJ14) 107 112
39: 292 type=196 (LJ14) 107 115
39: 293 type=193 (LJ14) 108 110
39: 294 type=193 (LJ14) 108 111
39: 295 type=196 (LJ14) 108 112
39: 296 type=196 (LJ14) 108 115
39: 297 type=197 (LJ14) 109 115
39: 298 type=194 (LJ14) 110 113
39: 299 type=194 (LJ14) 110 114
39: 300 type=194 (LJ14) 111 113
39: 301 type=194 (LJ14) 111 114
39: 302 type=196 (LJ14) 115 120
39: 303 type=197 (LJ14) 115 121
39: 304 type=198 (LJ14) 115 134
39: 305 type=190 (LJ14) 116 118
39: 306 type=195 (LJ14) 116 119
39: 307 type=186 (LJ14) 117 122
39: 308 type=186 (LJ14) 117 123
39: 309 type=187 (LJ14) 117 124
39: 310 type=188 (LJ14) 117 135
39: 311 type=189 (LJ14) 117 136
39: 312 type=190 (LJ14) 118 120
39: 313 type=190 (LJ14) 118 121
39: 314 type=190 (LJ14) 118 134
39: 315 type=191 (LJ14) 119 125
39: 316 type=192 (LJ14) 119 126
39: 317 type=192 (LJ14) 119 130
39: 318 type=190 (LJ14) 119 137
39: 319 type=192 (LJ14) 119 138
39: 320 type=193 (LJ14) 120 122
39: 321 type=193 (LJ14) 120 123
39: 322 type=191 (LJ14) 120 124
39: 323 type=194 (LJ14) 120 135
39: 324 type=186 (LJ14) 120 136
39: 325 type=191 (LJ14) 121 127
39: 326 type=191 (LJ14) 121 128
39: 327 type=191 (LJ14) 121 129
39: 328 type=191 (LJ14) 121 131
39: 329 type=191 (LJ14) 121 132
39: 330 type=191 (LJ14) 121 133
39: 331 type=195 (LJ14) 121 135
39: 332 type=187 (LJ14) 121 136
39: 333 type=193 (LJ14) 122 125
39: 334 type=191 (LJ14) 122 126
39: 335 type=191 (LJ14) 122 130
39: 336 type=196 (LJ14) 122 134
39: 337 type=193 (LJ14) 123 125
39: 338 type=191 (LJ14) 123 126
39: 339 type=191 (LJ14) 123 130
39: 340 type=196 (LJ14) 123 134
39: 341 type=197 (LJ14) 124 134
39: 342 type=193 (LJ14) 125 127
39: 343 type=193 (LJ14) 125 128
39: 344 type=193 (LJ14) 125 129
39: 345 type=193 (LJ14) 125 131
39: 346 type=193 (LJ14) 125 132
39: 347 type=193 (LJ14) 125 133
39: 348 type=191 (LJ14) 126 131
39: 349 type=191 (LJ14) 126 132
39: 350 type=191 (LJ14) 126 133
39: 351 type=191 (LJ14) 127 130
39: 352 type=191 (LJ14) 128 130
39: 353 type=191 (LJ14) 129 130
39: 354 type=196 (LJ14) 134 139
39: 355 type=197 (LJ14) 134 140
39: 356 type=198 (LJ14) 134 144
39: 357 type=190 (LJ14) 135 137
39: 358 type=195 (LJ14) 135 138
39: 359 type=186 (LJ14) 136 141
39: 360 type=186 (LJ14) 136 142
39: 361 type=186 (LJ14) 136 143
39: 362 type=188 (LJ14) 136 145
39: 363 type=189 (LJ14) 136 146
39: 364 type=190 (LJ14) 137 139
39: 365 type=190 (LJ14) 137 140
39: 366 type=190 (LJ14) 137 144
39: 367 type=190 (LJ14) 138 147
39: 368 type=192 (LJ14) 138 148
39: 369 type=193 (LJ14) 139 141
39: 370 type=193 (LJ14) 139 142
39: 371 type=193 (LJ14) 139 143
39: 372 type=194 (LJ14) 139 145
39: 373 type=186 (LJ14) 139 146
39: 374 type=195 (LJ14) 140 145
39: 375 type=187 (LJ14) 140 146
39: 376 type=196 (LJ14) 141 144
39: 377 type=196 (LJ14) 142 144
39: 378 type=196 (LJ14) 143 144
39: 379 type=196 (LJ14) 144 149
39: 380 type=197 (LJ14) 144 150
39: 381 type=198 (LJ14) 144 154
39: 382 type=190 (LJ14) 145 147
39: 383 type=195 (LJ14) 145 148
39: 384 type=186 (LJ14) 146 151
39: 385 type=186 (LJ14) 146 152
39: 386 type=186 (LJ14) 146 153
39: 387 type=188 (LJ14) 146 155
39: 388 type=190 (LJ14) 147 149
39: 389 type=190 (LJ14) 147 150
39: 390 type=190 (LJ14) 147 154
39: 391 type=193 (LJ14) 149 151
39: 392 type=193 (LJ14) 149 152
39: 393 type=193 (LJ14) 149 153
39: 394 type=194 (LJ14) 149 155
39: 395 type=195 (LJ14) 150 155
39: 396 type=196 (LJ14) 151 154
39: 397 type=196 (LJ14) 152 154
39: 398 type=196 (LJ14) 153 154
39: Coulomb-14:
39: nr: 0
39: LJC-14 q:
39: nr: 0
39: LJC Pairs NB:
39: nr: 0
39: LJ (SR):
39: nr: 0
39: Buck.ham (SR):
39: nr: 0
39: LJ (unused):
39: nr: 0
39: B.ham (unused):
39: nr: 0
39: Disper. corr.:
39: nr: 0
39: Coulomb (SR):
39: nr: 0
39: Coul (unused):
39: nr: 0
39: RF excl.:
39: nr: 0
39: Coul. recip.:
39: nr: 0
39: LJ recip.:
39: nr: 0
39: DPD:
39: nr: 0
39: Polarization:
39: nr: 0
39: Water Pol.:
39: nr: 0
39: Thole Pol.:
39: nr: 0
39: Anharm. Pol.:
39: nr: 0
39: Position Rest.:
39: nr: 0
39: Flat-bottom posres:
39: nr: 0
39: Dis. Rest.:
39: nr: 0
39: D.R.Viol. (nm):
39: nr: 0
39: Orient. Rest.:
39: nr: 0
39: Ori. R. RMSD:
39: nr: 0
39: Angle Rest.:
39: nr: 0
39: Angle Rest. Z:
39: nr: 0
39: Dih. Rest.:
39: nr: 0
39: Dih. Rest. Viol.:
39: nr: 0
39: Constraint:
39: nr: 0
39: Constr. No Conn.:
39: nr: 0
39: Settle:
39: nr: 0
39: Virtual site 2:
39: nr: 0
39: Virtual site 2fd:
39: nr: 0
39: Virtual site 3:
39: nr: 0
39: Virtual site 3fd:
39: nr: 0
39: Virtual site 3fad:
39: nr: 0
39: Virtual site 3out:
39: nr: 0
39: Virtual site 4fd:
39: nr: 0
39: Virtual site 4fdn:
39: nr: 0
39: Virtual site N:
39: nr: 0
39: COM Pull En.:
39: nr: 0
39: Density fitting:
39: nr: 0
39: Quantum En.:
39: nr: 0
39: Potential:
39: nr: 0
39: Kinetic En.:
39: nr: 0
39: Total Energy:
39: nr: 0
39: Conserved En.:
39: nr: 0
39: Temperature:
39: nr: 0
39: Vir. Temp. (not used):
39: nr: 0
39: Pres. DC:
39: nr: 0
39: Pressure:
39: nr: 0
39: dH/dl constr.:
39: nr: 0
39: dVremain/dl:
39: nr: 0
39: dEkin/dl:
39: nr: 0
39: dVcoul/dl:
39: nr: 0
39: dVvdw/dl:
39: nr: 0
39: dVbonded/dl:
39: nr: 0
39: dVrestraint/dl:
39: nr: 0
39: dVtemperature/dl:
39: nr: 0
39: grp[T-Coupling ] nr=1, name=[ rest]
39: grp[Energy Mon. ] nr=1, name=[ rest]
39: grp[Acceleration] nr=1, name=[ rest]
39: grp[Freeze ] nr=1, name=[ rest]
39: grp[User1 ] nr=1, name=[ rest]
39: grp[User2 ] nr=1, name=[ rest]
39: grp[VCM ] nr=1, name=[ rest]
39: grp[Compressed X] nr=1, name=[ rest]
39: grp[Or. Res. Fit] nr=1, name=[ rest]
39: grp[QMMM ] nr=1, name=[ rest]
39: grpname (11):
39: grpname[0]={name="System"}
39: grpname[1]={name="Protein"}
39: grpname[2]={name="Protein-H"}
39: grpname[3]={name="C-alpha"}
39: grpname[4]={name="Backbone"}
39: grpname[5]={name="MainChain"}
39: grpname[6]={name="MainChain+Cb"}
39: grpname[7]={name="MainChain+H"}
39: grpname[8]={name="SideChain"}
39: grpname[9]={name="SideChain-H"}
39: grpname[10]={name="rest"}
39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
39: allocated 0 0 0 0 0 0 0 0 0 0
39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
39: box (3x3):
39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
39: box_rel (3x3):
39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv (3x3):
39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev (3x3):
39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev (3x3):
39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev (3x3):
39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: nosehoover_xi: not available
39: x (156x3):
39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
39: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
39: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
39: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
39: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
39: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
39: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
39: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
39: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
39: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
39: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
39: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
39: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
39: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
39: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
39: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
39: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
39: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
39: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
39: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
39: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
39: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
39: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
39: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
39: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
39: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
39: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
39: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
39: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
39: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
39: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
39: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
39: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
39: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
39: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
39: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
39: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
39: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
39: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
39: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
39: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
39: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
39: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
39: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
39: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
39: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
39: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
39: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
39: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
39: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
39: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
39: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
39: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
39: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
39: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
39: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
39: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
39: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
39: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
39: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
39: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
39: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
39: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
39: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
39: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
39: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
39: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
39: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
39: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
39: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
39: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
39: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
39: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
39: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
39: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
39: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
39: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
39: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
39: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
39: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
39: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
39: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
39: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
39: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
39: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
39: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
39: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
39: v (156x3):
39: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: Group statistics
39: T-Coupling : 156 (total 156 atoms)
39: Energy Mon. : 156 (total 156 atoms)
39: Acceleration: 156 (total 156 atoms)
39: Freeze : 156 (total 156 atoms)
39: User1 : 156 (total 156 atoms)
39: User2 : 156 (total 156 atoms)
39: VCM : 156 (total 156 atoms)
39: Compressed X: 156 (total 156 atoms)
39: Or. Res. Fit: 156 (total 156 atoms)
39: QMMM : 156 (total 156 atoms)
39: [ OK ] DumpTest.WorksWithTpr (77 ms)
39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (2 ms)
39: [----------] 2 tests from DumpTest (79 ms total)
39:
39: [----------] 4 tests from ReportMethodsTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to 1570364735
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectInformation
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
39: [ OK ] ReportMethodsTest.WritesCorrectInformation (2 ms)
39: [ RUN ] ReportMethodsTest.ToolEndToEndTest
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
39: section: Methods
39: subsection: Simulation system
39: A system of 1 molecules (156 atoms) was simulated.
39:
39: subsection: Simulation settings
39: A total of 0 ns were simulated with a time step of 1 fs.
39: Neighbor searching was performed every 10 steps.
39: The Cut-off algorithm was used for electrostatic interactions.
39: with a cut-off of 1 nm.
39: A single cut-off of 1.1 nm was used for Van der Waals interactions.
39: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms)
39: [----------] 4 tests from ReportMethodsTest (3 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: trr version: GMX_trn_file (single precision)
39:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (6 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (7 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (5 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (33 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (3 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (13 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 18 tests from 4 test cases ran. (2438 ms total)
39: [ PASSED ] 18 tests.
39/54 Test #39: ToolUnitTests ....................... Passed 2.46 sec
test 40
Start 40: FileIOTests
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 33 tests from 8 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from FileMD5Test
40: [ RUN ] FileMD5Test.CanComputeMD5
40: [ OK ] FileMD5Test.CanComputeMD5 (1 ms)
40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
40: [----------] 2 tests from FileMD5Test (2 ms total)
40:
40: [----------] 3 tests from MrcSerializer
40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (5 ms)
40: [----------] 3 tests from MrcSerializer (5 ms total)
40:
40: [----------] 4 tests from MrcDensityMap
40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (6 ms)
40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms)
40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms)
40: [----------] 4 tests from MrcDensityMap (9 ms total)
40:
40: [----------] 8 tests from MrcDensityMapHeaderTest
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.IsSane
40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
40: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
40:
40: [----------] 9 tests from ReadTest
40: [ RUN ] ReadTest.get_eint_ReadsInteger
40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_eint64_ReadsInteger
40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsInteger
40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsFloat
40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
40: [ RUN ] ReadTest.get_ereal_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not a
40: real value
40:
40:
40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
40: [----------] 9 tests from ReadTest (0 ms total)
40:
40: [----------] 1 test from FileIOXdrSerializerTest
40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms)
40: [----------] 1 test from FileIOXdrSerializerTest (1 ms total)
40:
40: [----------] 2 tests from TngTest
40: [ RUN ] TngTest.CanOpenTngFile
40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
40: [ OK ] TngTest.CanOpenTngFile (0 ms)
40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
40: [----------] 2 tests from TngTest (0 ms total)
40:
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (2 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (4 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms)
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (8 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 33 tests from 8 test cases ran. (26 ms total)
40: [ PASSED ] 33 tests.
40/54 Test #40: FileIOTests ......................... Passed 0.05 sec
test 41
Start 41: SelectionUnitTests
41: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 192 tests from 11 test cases.
41: [----------] Global test environment set-up.
41: [----------] 1 test from IndexGroupTest
41: [ RUN ] IndexGroupTest.RemovesDuplicates
41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
41: [----------] 1 test from IndexGroupTest (0 ms total)
41:
41: [----------] 15 tests from IndexBlockTest
41: [ RUN ] IndexBlockTest.CreatesUnknownBlock
41: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms)
41: [ RUN ] IndexBlockTest.CreatesAtomBlock
41: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesSingleBlock
41: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
41: [----------] 15 tests from IndexBlockTest (3 ms total)
41:
41: [----------] 11 tests from IndexMapTest
41: [ RUN ] IndexMapTest.InitializesAtomBlock
41: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
41: [ RUN ] IndexMapTest.InitializesMoleculeBlock
41: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
41: [ RUN ] IndexMapTest.MapsSingleBlock
41: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocks
41: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms)
41: [ RUN ] IndexMapTest.HandlesMultipleRequests
41: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms)
41: [----------] 11 tests from IndexMapTest (5 ms total)
41:
41: [----------] 3 tests from IndexGroupsAndNamesTest
41: [ RUN ] IndexGroupsAndNamesTest.containsNames
41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms)
41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
41: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
41:
41: [----------] 15 tests from NeighborhoodSearchTest
41: [ RUN ] NeighborhoodSearchTest.SimpleSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSearch (35 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (36 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchBox
41: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (21 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (10 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (6 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (5 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (1 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (101 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (8 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (2 ms)
41: [----------] 15 tests from NeighborhoodSearchTest (230 ms total)
41:
41: [----------] 12 tests from PositionCalculationTest
41: [ RUN ] PositionCalculationTest.ComputesAtomPositions
41: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionMask
41: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms)
41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
41: [----------] 12 tests from PositionCalculationTest (6 ms total)
41:
41: [----------] 29 tests from SelectionCollectionTest
41: [ RUN ] SelectionCollectionTest.HandlesNoSelections
41: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
41: [----------] 29 tests from SelectionCollectionTest (36 ms total)
41:
41: [----------] 14 tests from SelectionCollectionInteractiveTest
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
41: [----------] 14 tests from SelectionCollectionInteractiveTest (23 ms total)
41:
41: [----------] 66 tests from SelectionCollectionDataTest
41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResnr
41: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesChain
41: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMass
41: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCharge
41: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBeta
41: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResname
41: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (16 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (12 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (14 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (6 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (13 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (5 ms)
41: [----------] 66 tests from SelectionCollectionDataTest (322 ms total)
41:
41: [----------] 17 tests from SelectionOptionTest
41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms)
41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptySelections
41: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelections
41: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesAdjuster
41: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
41: [----------] 17 tests from SelectionOptionTest (14 ms total)
41:
41: [----------] 9 tests from SelectionFileOptionTest
41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
41: [----------] 9 tests from SelectionFileOptionTest (7 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 192 tests from 11 test cases ran. (648 ms total)
41: [ PASSED ] 192 tests.
41/54 Test #41: SelectionUnitTests .................. Passed 0.68 sec
test 42
Start 42: MdrunOutputTests
42: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml"
42: Test timeout computed to be: 600
42: [==========] Running 12 tests from 5 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from MdrunTest
42: [ RUN ] MdrunTest.WritesHelp
42: [ OK ] MdrunTest.WritesHelp (5 ms)
42: [----------] 1 test from MdrunTest (5 ms total)
42:
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
42: Setting the LD random seed to 1528724293
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.204 0.102 199.4
42: (ns/day) (hour/ns)
42: Performance: 1.691 14.195
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (145 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
42: Setting the LD random seed to -2164493
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.220 0.110 199.4
42: (ns/day) (hour/ns)
42: Performance: 1.566 15.327
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (133 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
42: Setting the LD random seed to -545429025
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.221 0.111 199.5
42: (ns/day) (hour/ns)
42: Performance: 1.561 15.374
42:
Reading frame 0 time 0.000
42: # Atoms 3
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (133 ms)
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (412 ms total)
42:
42: [----------] 2 tests from Argon12/OutputFiles
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.238 0.119 199.5
42: (ns/day) (hour/ns)
42: Performance: 12.297 1.952
42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (141 ms)
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.208 0.104 199.6
42: (ns/day) (hour/ns)
42: Performance: 14.071 1.706
42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (125 ms)
42: [----------] 2 tests from Argon12/OutputFiles (266 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/Trajectories
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
42: Setting the LD random seed to 1876426722
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.531 0.266 199.7
42: (ns/day) (hour/ns)
42: Performance: 2.277 10.542
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (293 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
42: Setting the LD random seed to 661516687
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.163 0.082 199.2
42: (ns/day) (hour/ns)
42: Performance: 7.405 3.241
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (108 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
42: Setting the LD random seed to -1746272474
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.148 0.074 199.2
42: (ns/day) (hour/ns)
42: Performance: 8.153 2.944
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (100 ms)
42: [----------] 3 tests from MdrunCanWrite/Trajectories (501 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
42: Setting the LD random seed to -3342344
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.165 0.083 199.3
42: (ns/day) (hour/ns)
42: Performance: 3.129 7.669
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (108 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
42: Setting the LD random seed to 1879027679
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.166 0.084 199.1
42: (ns/day) (hour/ns)
42: Performance: 3.104 7.732
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (109 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
42: Setting the LD random seed to -16909140
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.148 0.074 199.0
42: (ns/day) (hour/ns)
42: Performance: 3.487 6.882
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (100 ms)
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (317 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 12 tests from 5 test cases ran. (1501 ms total)
42: [ PASSED ] 12 tests.
42/54 Test #42: MdrunOutputTests .................... Passed 1.52 sec
test 43
Start 43: MdrunModulesTests
43: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 10 tests from 3 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to -321192034
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.85654101644806e+03
43: Maximum force = 2.88468568366558e+03 on atom 3
43: Norm of force = 1.07544474716821e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (46 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to -556105877
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.71386626596691e+04
43: Maximum force = 4.34097106676756e+03 on atom 2
43: Norm of force = 1.25497916295893e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (26 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (18 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to 1593372587
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.161 0.081 199.4
43: (ns/day) (hour/ns)
43: Performance: 3.214 7.468
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.147 0.074 199.3
43: (ns/day) (hour/ns)
43: Performance: 5.862 4.094
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (187 ms)
43: [----------] 4 tests from DensityFittingTest (277 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -69230469
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 175.3
43: (ns/day) (hour/ns)
43: Performance: 93.039 0.258
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (22 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -8262
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 173.7
43: (ns/day) (hour/ns)
43: Performance: 97.521 0.246
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (23 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1174097759
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 175.5
43: (ns/day) (hour/ns)
43: Performance: 94.816 0.253
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (22 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -336076870
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.001 183.2
43: (ns/day) (hour/ns)
43: Performance: 59.079 0.406
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (72 ms)
43: [----------] 4 tests from MimicTest (139 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to -704847874
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 59431.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.270 0.135 199.4
43: (ns/day) (hour/ns)
43: Performance: 3.831 6.265
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (593 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to 1814007462
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 41675.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.19770464690297e+03
43: Maximum force = 1.77948604657896e+04 on atom 9
43: Norm of force = 7.87328617833980e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (457 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (1050 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 10 tests from 3 test cases ran. (1466 ms total)
43: [ PASSED ] 10 tests.
43/54 Test #43: MdrunModulesTests ................... Passed 1.49 sec
test 44
Start 44: MdrunIOTests
44: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunIOTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 51 tests from 9 test cases.
44: [----------] Global test environment set-up.
44: [----------] 3 tests from GromppTest
44: [ RUN ] GromppTest.EmptyMdpFileWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -9454499
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.EmptyMdpFileWorks (10 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -1208123729
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group rest: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorks (9 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -1092878341
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group Methanol: Single, 3 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 3.0 280.0
44: 6.0- 270.0
44: Simulated annealing for group SOL: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group Methanol is 7.20
44: Number of degrees of freedom in T-Coupling group SOL is 4.80
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (10 ms)
44: [----------] 3 tests from GromppTest (29 ms total)
44:
44: [----------] 6 tests from MdrunTerminationTest
44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
44: Setting the LD random seed to 730197931
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.190 0.095 199.4
44: (ns/day) (hour/ns)
44: Performance: 2.719 8.825
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.129 0.065 199.2
44: (ns/day) (hour/ns)
44: Performance: 4.008 5.988
44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (213 ms)
44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
44: Setting the LD random seed to -84542599
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 1, rlist from 1.024 to 1
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 100 steps, 0.1 ps.
44:
44: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.152 0.076 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.403 7.052
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Setting nsteps to 102
44: Writing statusfile with starting step 0 and length 102 steps...
44: time 0.000 and length 0.102 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.162 0.081 199.3
44: (ns/day) (hour/ns)
44: Performance: 107.425 0.223
44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (192 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
44: Setting the LD random seed to 1869557757
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.169 0.085 199.4
44: (ns/day) (hour/ns)
44: Performance: 3.065 7.830
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.161 0.081 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.207 7.484
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Setting nsteps to 6
44: Writing statusfile with starting step 0 and length 6 steps...
44: time 0.000 and length 0.006 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.156 0.078 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.311 7.249
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Setting nsteps to 8
44: Writing statusfile with starting step 0 and length 8 steps...
44: time 0.000 and length 0.008 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.145 0.073 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.564 6.733
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.001 0.001 159.2
44: (ns/day) (hour/ns)
44: Performance: 117.582 0.204
44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (384 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
44: Setting the LD random seed to -1094189157
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.168 0.084 199.4
44: (ns/day) (hour/ns)
44: Performance: 3.083 7.784
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.163 0.082 199.3
44: (ns/day) (hour/ns)
44: Performance: 5.266 4.557
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (199 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
44: Setting the LD random seed to -676881185
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.137 0.069 199.2
44: (ns/day) (hour/ns)
44: Performance: 3.783 6.345
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (93 ms)
44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
44: Setting the LD random seed to -1644302344
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.150 0.075 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.446 6.965
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.145 0.073 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.559 6.743
44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (181 ms)
44: [----------] 6 tests from MdrunTerminationTest (1262 ms total)
44:
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.232 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.620 1.902
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.626 3.622
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.265 0.133 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.849 4.103
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (423 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.271 0.136 199.7
44: (ns/day) (hour/ns)
44: Performance: 10.806 2.221
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.219 0.110 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.093 3.384
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.233 0.117 199.7
44: (ns/day) (hour/ns)
44: Performance: 6.657 3.605
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (416 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.236 0.118 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.422 1.932
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.301 0.151 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.159 4.652
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.265 0.133 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.849 4.103
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (458 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.253 0.127 199.6
44: (ns/day) (hour/ns)
44: Performance: 11.594 2.070
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.301 0.151 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.162 4.649
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.703 3.581
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (450 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.250 0.126 199.5
44: (ns/day) (hour/ns)
44: Performance: 11.701 2.051
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.251 0.126 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.191 3.877
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.249 0.125 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.240 3.846
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (433 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.253 0.126 199.7
44: (ns/day) (hour/ns)
44: Performance: 11.612 2.067
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.235 0.118 199.7
44: (ns/day) (hour/ns)
44: Performance: 6.599 3.637
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.233 0.117 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.651 3.609
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (416 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.232 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.619 1.902
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.233 0.117 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.662 3.603
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.712 3.576
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (409 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.250 0.125 199.5
44: (ns/day) (hour/ns)
44: Performance: 11.727 2.047
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.250 0.125 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.203 3.869
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.708 3.578
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (424 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.225 0.113 199.2
44: (ns/day) (hour/ns)
44: Performance: 13.026 1.842
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.241 0.121 199.3
44: (ns/day) (hour/ns)
44: Performance: 6.425 3.735
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.238 0.119 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.508 3.688
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (520 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.251 0.126 199.4
44: (ns/day) (hour/ns)
44: Performance: 11.662 2.058
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.208 0.104 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.446 3.223
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.271 0.136 199.4
44: (ns/day) (hour/ns)
44: Performance: 5.718 4.197
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (533 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.267 0.134 199.3
44: (ns/day) (hour/ns)
44: Performance: 10.978 2.186
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.207 0.104 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.499 3.200
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.219 0.110 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.068 3.396
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (592 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.3
44: (ns/day) (hour/ns)
44: Performance: 12.666 1.895
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.222 0.111 199.2
44: (ns/day) (hour/ns)
44: Performance: 6.989 3.434
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.219 0.110 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.090 3.385
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (559 ms)
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (5634 ms total)
44:
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.329 0.165 199.4
44: (ns/day) (hour/ns)
44: Performance: 8.893 2.699
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.271 0.136 198.9
44: (ns/day) (hour/ns)
44: Performance: 5.710 4.203
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.565 0.283 199.7
44: (ns/day) (hour/ns)
44: Performance: 2.748 8.735
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (759 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.471 0.236 199.7
44: (ns/day) (hour/ns)
44: Performance: 6.234 3.850
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.291 0.146 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.337 4.497
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.291 0.146 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.329 4.504
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (700 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.372 0.186 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.876 3.047
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.326 0.164 199.3
44: (ns/day) (hour/ns)
44: Performance: 4.751 5.051
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.290 0.146 199.3
44: (ns/day) (hour/ns)
44: Performance: 5.342 4.493
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (758 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.312 0.156 199.4
44: (ns/day) (hour/ns)
44: Performance: 9.401 2.553
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.285 0.143 199.2
44: (ns/day) (hour/ns)
44: Performance: 5.436 4.415
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.264 0.132 199.3
44: (ns/day) (hour/ns)
44: Performance: 5.873 4.086
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (658 ms)
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2875 ms total)
44:
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.227 0.114 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.934 1.856
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.631 3.619
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.214 3.327
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (396 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.102 199.5
44: (ns/day) (hour/ns)
44: Performance: 14.425 1.664
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.133 3.365
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.221 3.324
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (375 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.102 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.426 1.664
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.093 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.405 2.855
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.206 3.331
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (358 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.286 0.143 199.5
44: (ns/day) (hour/ns)
44: Performance: 10.236 2.345
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.284 0.142 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.467 4.390
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.241 3.314
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (450 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.221 0.111 199.6
44: (ns/day) (hour/ns)
44: Performance: 13.246 1.812
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.101 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.662 3.133
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.199 0.100 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.799 3.077
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (367 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.252 0.126 199.5
44: (ns/day) (hour/ns)
44: Performance: 11.617 2.066
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.625 3.623
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.236 3.317
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (408 ms)
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (2354 ms total)
44:
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.236 0.118 199.4
44: (ns/day) (hour/ns)
44: Performance: 12.409 1.934
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.718 3.110
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.232 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.700 3.582
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (393 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.517 1.776
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.131 3.365
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.706 3.579
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (392 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.216 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.550 1.771
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.723 3.108
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.833 3.064
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (366 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.102 199.6
44: (ns/day) (hour/ns)
44: Performance: 14.446 1.661
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.219 0.110 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.089 3.386
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.216 0.108 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.184 3.341
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (375 ms)
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (1527 ms total)
44:
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.699 1.890
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.150 3.357
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.834 3.064
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (382 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.524 1.775
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.629 3.620
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.724 3.569
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (400 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.300 0.150 199.6
44: (ns/day) (hour/ns)
44: Performance: 9.783 2.453
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.143 3.360
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.233 3.318
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (424 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.218 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.426 1.788
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.479 2.830
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.230 0.115 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.736 3.563
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (375 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.199 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.724 1.630
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.136 3.363
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.838 3.062
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (365 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.471 1.782
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.733 3.103
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.560 2.804
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (359 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.3
44: (ns/day) (hour/ns)
44: Performance: 14.654 1.638
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.141 3.361
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.197 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.860 3.053
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (366 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.526 1.774
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.736 3.102
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.197 0.099 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.860 3.054
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (366 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.186 0.093 199.5
44: (ns/day) (hour/ns)
44: Performance: 15.760 1.523
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.671 3.129
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.233 0.117 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.668 3.599
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (367 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms)
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (3408 ms total)
44:
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.232 0.116 199.4
44: (ns/day) (hour/ns)
44: Performance: 12.618 1.902
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.136 3.363
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.196 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.894 3.040
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (382 ms)
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (382 ms total)
44:
44: [----------] 3 tests from Checking/InitialConstraintsTest
44: [ RUN ] Checking/InitialConstraintsTest.Works/0
44: Setting the LD random seed to -33650690
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.170 0.085 199.2
44: (ns/day) (hour/ns)
44: Performance: 2.026 11.848
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (111 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/1
44: Setting the LD random seed to -402928897
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.168 0.084 199.4
44: (ns/day) (hour/ns)
44: Performance: 2.048 11.719
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (108 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: Integrator method md-vv-avek is implemented primarily for validation
44: purposes; for molecular dynamics, you should probably be using md or md-vv
44:
44: Setting the LD random seed to 905829626
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.166 0.084 199.2
44: (ns/day) (hour/ns)
44: Performance: 2.068 11.603
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (108 ms)
44: [----------] 3 tests from Checking/InitialConstraintsTest (327 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 51 tests from 9 test cases ran. (17798 ms total)
44: [ PASSED ] 51 tests.
44/54 Test #44: MdrunIOTests ........................ Passed 17.84 sec
test 45
Start 45: MdrunTests
45: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 24 tests from 7 test cases.
45: [----------] Global test environment set-up.
45: [----------] 1 test from DispersionCorrectionTest
45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to -571220001
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
45: Cleaning up constraints and constant bonded interactions with virtual sites
45: Converted 3 Bonds with virtual sites to connections, 7 left
45: Removed 18 Angles with virtual sites, 21 left
45: Removed 10 Proper Dih.s with virtual sites, 44 left
45: Converted 12 Constraints with virtual sites to connections, 0 left
45: Number of degrees of freedom in T-Coupling group System is 30.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: There are 9 non-linear virtual site constructions. Their contribution to
45: the energy error is approximated. In most cases this does not affect the
45: error significantly.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 10 to 50, rlist from 1.016 to 1.167
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Alanine dipeptide in vacuo'
45: 200 steps, 0.4 ps.
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.354 0.177 199.6
45: (ns/day) (hour/ns)
45: Performance: 195.740 0.123
45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (267 ms)
45: [----------] 1 test from DispersionCorrectionTest (267 ms total)
45:
45: [----------] 1 test from OriresTest
45: [ RUN ] OriresTest.OriresCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to -1109394195
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 518.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
45: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
45:
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
45: 10 steps, 0.0 ps.
45: turning H bonds into constraints...
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.325 0.163 199.5
45: (ns/day) (hour/ns)
45: Performance: 11.655 2.059
45: [ OK ] OriresTest.OriresCanRun (850 ms)
45: [----------] 1 test from OriresTest (851 ms total)
45:
45: [----------] 3 tests from PmeTest
45: [ RUN ] PmeTest.ReproducesEnergies
45: Setting the LD random seed to -69600337
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.328 0.164 199.6
45: (ns/day) (hour/ns)
45: Performance: 11.037 2.174
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.284 0.142 199.6
45: (ns/day) (hour/ns)
45: Performance: 12.739 1.884
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45:
45: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.267 0.134 199.6
45: (ns/day) (hour/ns)
45: Performance: 13.585 1.767
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (539 ms)
45: [ RUN ] PmeTest.ScalesTheBox
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1772091070
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.005 0.003 180.0
45: (ns/day) (hour/ns)
45: Performance: 30.698 0.782
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBox (37 ms)
45: [ RUN ] PmeTest.ScalesTheBoxWithWalls
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -143524082
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Searching the wall atom type(s)
45: Number of degrees of freedom in T-Coupling group rest is 13.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: NVE simulation: will use the initial temperature of 966.268 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.018 0.009 190.9
45: (ns/day) (hour/ns)
45: Performance: 9.226 2.601
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBoxWithWalls (74 ms)
45: [----------] 3 tests from PmeTest (650 ms total)
45:
45: [----------] 1 test from CompelTest
45: [ RUN ] CompelTest.SwapCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to -146801826
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 1 bonded neighbours molecule type 'NA'
45: Excluding 1 bonded neighbours molecule type 'CL'
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Split0 group 'Ch0' contains 83 atoms.
45: Split1 group 'Ch1' contains 83 atoms.
45: Solvent group 'SOL' contains 11931 atoms.
45: Swap group 'NA+' contains 19 atoms.
45: Swap group 'CL-' contains 19 atoms.
45: Number of degrees of freedom in T-Coupling group System is 27869.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: Removing center of mass motion in the presence of position restraints
45: might cause artifacts. When you are using position restraints to
45: equilibrate a macro-molecule, the artifacts are usually negligible.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Determining initial numbers of ions per compartment.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 2 steps, 0.0 ps.
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 1 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 2.886 1.444 199.9
45: (ns/day) (hour/ns)
45: Performance: 0.898 26.735
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Copying channel fluxes from checkpoint file data
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 2.573 1.287 199.9
45: (ns/day) (hour/ns)
45: Performance: 1.007 23.830
45: [ OK ] CompelTest.SwapCanRun (6268 ms)
45: [----------] 1 test from CompelTest (6268 ms total)
45:
45: [----------] 6 tests from BondedInteractionsTest
45: [ RUN ] BondedInteractionsTest.NormalBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1373984751
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 177.3
45: (ns/day) (hour/ns)
45: Performance: 96.482 0.249
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalBondWorks (22 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -25690991
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 177.0
45: (ns/day) (hour/ns)
45: Performance: 102.922 0.233
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (26 ms)
45: [ RUN ] BondedInteractionsTest.NormalAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -337772702
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 176.4
45: (ns/day) (hour/ns)
45: Performance: 104.344 0.230
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalAngleWorks (21 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -539022346
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 177.4
45: (ns/day) (hour/ns)
45: Performance: 103.688 0.231
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (24 ms)
45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -19072899
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 177.3
45: (ns/day) (hour/ns)
45: Performance: 103.955 0.231
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (21 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -297818145
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 177.7
45: (ns/day) (hour/ns)
45: Performance: 101.880 0.236
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (27 ms)
45: [----------] 6 tests from BondedInteractionsTest (142 ms total)
45:
45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.347 0.174 199.8
45: (ns/day) (hour/ns)
45: Performance: 8.464 2.835
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.301 0.151 199.6
45: (ns/day) (hour/ns)
45: Performance: 9.743 2.463
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision)
45:
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (366 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.249 0.125 199.7
45: (ns/day) (hour/ns)
45: Performance: 11.786 2.036
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.268 0.134 199.6
45: (ns/day) (hour/ns)
45: Performance: 10.951 2.191
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (300 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.348 0.174 199.8
45: (ns/day) (hour/ns)
45: Performance: 8.420 2.850
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.245 0.123 199.5
45: (ns/day) (hour/ns)
45: Performance: 11.949 2.009
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (2860 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.300 0.150 199.7
45: (ns/day) (hour/ns)
45: Performance: 9.784 2.453
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.245 0.123 199.5
45: (ns/day) (hour/ns)
45: Performance: 11.985 2.002
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (2825 ms)
45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (6351 ms total)
45:
45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.258 0.129 199.6
45: (ns/day) (hour/ns)
45: Performance: 11.370 2.111
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.237 0.119 199.7
45: (ns/day) (hour/ns)
45: Performance: 12.392 1.937
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (289 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.247 0.124 199.5
45: (ns/day) (hour/ns)
45: Performance: 11.882 2.020
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.220 0.110 199.6
45: (ns/day) (hour/ns)
45: Performance: 13.341 1.799
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (276 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.226 0.113 199.5
45: (ns/day) (hour/ns)
45: Performance: 12.941 1.855
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.220 0.110 199.7
45: (ns/day) (hour/ns)
45: Performance: 13.329 1.801
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (265 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.212 0.107 199.4
45: (ns/day) (hour/ns)
45: Performance: 13.789 1.741
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.253 0.127 199.7
45: (ns/day) (hour/ns)
45: Performance: 11.589 2.071
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (276 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: Non-default thread affinity set probably by the OpenMP library,
45: disabling internal thread affinity
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.294 0.147 199.6
45: (ns/day) (hour/ns)
45: Performance: 9.963 2.409
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.248 0.124 199.7
45: (ns/day) (hour/ns)
45: Performance: 11.830 2.029
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (2826 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.334 0.168 199.5
45: (ns/day) (hour/ns)
45: Performance: 8.769 2.737
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.231 0.116 199.6
45: (ns/day) (hour/ns)
45: Performance: 12.683 1.892
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (2842 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.290 0.145 199.6
45: (ns/day) (hour/ns)
45: Performance: 10.107 2.375
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.214 0.107 199.6
45: (ns/day) (hour/ns)
45: Performance: 13.711 1.750
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (2807 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.229 0.115 199.4
45: (ns/day) (hour/ns)
45: Performance: 12.800 1.875
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.231 0.116 199.6
45: (ns/day) (hour/ns)
45: Performance: 12.709 1.888
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (2792 ms)
45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (12374 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 24 tests from 7 test cases ran. (26905 ms total)
45: [ PASSED ] 24 tests.
45/54 Test #45: MdrunTests .......................... Passed 26.94 sec
test 46
Start 46: MdrunNonIntegratorTests
46: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 65 tests from 7 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from NonbondedBenchTest
46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
46: System size: 3000 atoms
46: Cut-off radius: 1 nm
46: Number of threads: 1
46: Number of iterations: 1
46: Compute energies: no
46: Ewald excl. corr.: analytical
46:
46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
46: total useful
46: Ewald all geom. no 0.000 0.0000 inf inf
46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (254 ms)
46: [----------] 1 test from NonbondedBenchTest (254 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.79910463671071e+01
46: Maximum force = 1.86297359432220e+02 on atom 13
46: Norm of force = 8.77219865482161e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1088 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.58622538633290e+01
46: Maximum force = 4.27274822366523e+02 on atom 13
46: Norm of force = 1.84530029253828e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2533 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19376899751521e+02
46: Maximum force = 9.99884921009767e+03 on atom 9
46: Norm of force = 4.61669565054298e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (445 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.51743018140925e+02
46: Maximum force = 7.42089573409111e+03 on atom 9
46: Norm of force = 3.56929298615739e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (445 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.56984193848276e+02
46: Maximum force = 4.56923624626296e+02 on atom 17
46: Norm of force = 1.83258377168331e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (72 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06800e+03 on atom 28
46: F-Norm = 4.26922e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.69410778678185e+02
46: Maximum force = 2.18225948473957e+02 on atom 17
46: Norm of force = 7.92068036537697e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (74 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4657 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.74257075835450e-01
46: Maximum force = 4.01322929015108e+00 on atom 1
46: Norm of force = 1.63839399694368e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (24 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.90642313893957e-01
46: Maximum force = 2.57812909491105e+00 on atom 1
46: Norm of force = 1.05251679559258e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (24 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.90642313893957e-01
46: Maximum force = 2.57812909491105e+00 on atom 1
46: Norm of force = 1.05251679559258e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (25 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19395484891517e+02
46: Maximum force = 9.97041707197910e+03 on atom 9
46: Norm of force = 4.62274878665467e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (450 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.56258793899479e+02
46: Maximum force = 7.50181017480397e+03 on atom 9
46: Norm of force = 3.61390332564874e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (448 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 5.61116097794203e+02
46: Maximum force = 1.26854826291223e+04 on atom 10
46: Norm of force = 6.06436286976271e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (456 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1428 ms total)
46:
46: [----------] 5 tests from NormalModesWorks/NormalModesTest
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 3 of the 3 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation '2 scaled waters'
46: 12 steps.
46:
46: Maximum force: 9.96989e-06
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.5-Raspbian-2020.5-4
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (33 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
46:
46: NOTE 3 [file villin.top, line 2452]:
46: System has non-zero total charge: -2.000000
46: Total charge should normally be an integer. See
46: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
46: for discussion on how close it should be to an integer.
46:
46:
46:
46: Number of degrees of freedom in T-Coupling group System is 765.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=256), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN'
46: 512 steps.
46:
46: Maximum force: 6.97568e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.5-Raspbian-2020.5-4
46:
46: Diagonalizing to find vectors 7 through 50...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--50 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 256 Atoms
46: Using begin = 7 and end = 50
46: Full matrix storage format, nrow=768, ncols=768
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (9877 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'flex spc dimer'
46: 12 steps.
46:
46: Maximum force: 3.36401e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.5-Raspbian-2020.5-4
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (2529 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Number of degrees of freedom in T-Coupling group System is 6.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=3), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation '1 TIP5P'
46: 6 steps.
46:
46: Maximum force: 2.42882e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.5-Raspbian-2020.5-4
46:
46: Diagonalizing to find vectors 7 through 9...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--9 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 3 Atoms
46: There are: 2 VSites
46: Using begin = 7 and end = 9
46: Full matrix storage format, nrow=9, ncols=9
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (2519 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 6 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SW'
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'sw dimer'
46: 12 steps.
46:
46: Maximum force: 1.07599e-03
46: The force is probably not small enough to ensure that you are at a minimum.
46: Be aware that negative eigenvalues may occur
46: when the resulting matrix is diagonalized.
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.5-Raspbian-2020.5-4
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: There are: 2 Shells
46: There are: 2 VSites
46:
46: NOTE: in the current version shell prediction during the crun is disabled
46:
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (33 ms)
46: [----------] 5 tests from NormalModesWorks/NormalModesTest (14993 ms total)
46:
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.279 0.140 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.500 2.286
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
46:
46: trr version: GMX_trn_file (double precision)
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.006 196.4
46: (ns/day) (hour/ns)
46: Performance: 226.069 0.106
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (189 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.372 0.186 199.8
46: (ns/day) (hour/ns)
46: Performance: 7.890 3.042
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 196.1
46: (ns/day) (hour/ns)
46: Performance: 236.409 0.102
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (232 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.654 0.327 199.8
46: (ns/day) (hour/ns)
46: Performance: 4.486 5.350
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 196.1
46: (ns/day) (hour/ns)
46: Performance: 234.030 0.103
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (375 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.388 0.194 199.7
46: (ns/day) (hour/ns)
46: Performance: 7.560 3.175
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 196.0
46: (ns/day) (hour/ns)
46: Performance: 231.871 0.104
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (242 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.220 0.110 199.4
46: (ns/day) (hour/ns)
46: Performance: 13.316 1.802
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 196.2
46: (ns/day) (hour/ns)
46: Performance: 206.157 0.116
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2663 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.259 0.130 199.7
46: (ns/day) (hour/ns)
46: Performance: 11.309 2.122
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 196.2
46: (ns/day) (hour/ns)
46: Performance: 204.250 0.118
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (2676 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.259 0.130 199.5
46: (ns/day) (hour/ns)
46: Performance: 11.321 2.120
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 196.3
46: (ns/day) (hour/ns)
46: Performance: 201.735 0.119
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (2674 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.237 0.119 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.337 1.945
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 196.2
46: (ns/day) (hour/ns)
46: Performance: 205.005 0.117
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (2650 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.197 0.099 199.2
46: (ns/day) (hour/ns)
46: Performance: 14.815 1.620
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.024 0.012 196.8
46: (ns/day) (hour/ns)
46: Performance: 120.905 0.199
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (212 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.256 0.128 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.449 2.096
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.024 0.012 196.7
46: (ns/day) (hour/ns)
46: Performance: 121.248 0.198
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (242 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.271 0.136 199.4
46: (ns/day) (hour/ns)
46: Performance: 10.806 2.221
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.024 0.012 196.8
46: (ns/day) (hour/ns)
46: Performance: 120.494 0.199
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (301 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.287 0.144 199.4
46: (ns/day) (hour/ns)
46: Performance: 10.207 2.351
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.025 0.013 196.7
46: (ns/day) (hour/ns)
46: Performance: 117.336 0.205
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (293 ms)
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (12749 ms total)
46:
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.331 0.166 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.840 2.715
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.6
46: (ns/day) (hour/ns)
46: Performance: 93.373 0.257
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (291 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.332 0.166 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.830 2.718
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.6
46: (ns/day) (hour/ns)
46: Performance: 94.157 0.255
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (291 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.299 0.150 199.3
46: (ns/day) (hour/ns)
46: Performance: 9.794 2.451
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.8
46: (ns/day) (hour/ns)
46: Performance: 93.342 0.257
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (275 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.465 0.233 199.6
46: (ns/day) (hour/ns)
46: Performance: 6.309 3.804
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.8
46: (ns/day) (hour/ns)
46: Performance: 93.957 0.255
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (359 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.314 0.157 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.326 2.573
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.5
46: (ns/day) (hour/ns)
46: Performance: 93.575 0.256
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.348 0.175 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.415 2.852
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.5
46: (ns/day) (hour/ns)
46: Performance: 93.909 0.256
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (300 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.399 0.200 199.5
46: (ns/day) (hour/ns)
46: Performance: 7.345 3.267
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.6
46: (ns/day) (hour/ns)
46: Performance: 93.784 0.256
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (325 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.281 0.141 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.407 2.306
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.7
46: (ns/day) (hour/ns)
46: Performance: 93.652 0.256
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (266 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.350 0.175 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.370 2.867
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.8
46: (ns/day) (hour/ns)
46: Performance: 93.405 0.257
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (300 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.449 0.225 199.6
46: (ns/day) (hour/ns)
46: Performance: 6.523 3.679
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.8
46: (ns/day) (hour/ns)
46: Performance: 93.809 0.256
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (350 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.334 0.167 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.780 2.733
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.5
46: (ns/day) (hour/ns)
46: Performance: 96.076 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (291 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.390 0.195 199.7
46: (ns/day) (hour/ns)
46: Performance: 7.530 3.187
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.8
46: (ns/day) (hour/ns)
46: Performance: 96.619 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (317 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.388 0.195 199.7
46: (ns/day) (hour/ns)
46: Performance: 7.549 3.179
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.0
46: (ns/day) (hour/ns)
46: Performance: 96.947 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (316 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.307 0.154 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.540 2.516
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.6
46: (ns/day) (hour/ns)
46: Performance: 95.455 0.251
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (276 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.322 0.161 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.108 2.635
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.2
46: (ns/day) (hour/ns)
46: Performance: 95.774 0.251
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.471 0.236 199.7
46: (ns/day) (hour/ns)
46: Performance: 6.225 3.855
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.9
46: (ns/day) (hour/ns)
46: Performance: 96.944 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (358 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.573 0.287 199.8
46: (ns/day) (hour/ns)
46: Performance: 5.119 4.688
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.9
46: (ns/day) (hour/ns)
46: Performance: 97.290 0.247
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (407 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.474 0.237 199.8
46: (ns/day) (hour/ns)
46: Performance: 6.186 3.880
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 95.271 0.252
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (359 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.373 0.187 199.7
46: (ns/day) (hour/ns)
46: Performance: 7.863 3.052
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.8
46: (ns/day) (hour/ns)
46: Performance: 96.675 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (308 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.308 0.154 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.517 2.522
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.2
46: (ns/day) (hour/ns)
46: Performance: 96.383 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (276 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.405 0.203 199.7
46: (ns/day) (hour/ns)
46: Performance: 7.247 3.312
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.6
46: (ns/day) (hour/ns)
46: Performance: 95.758 0.251
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (325 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.338 0.169 199.6
46: (ns/day) (hour/ns)
46: Performance: 8.682 2.764
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.7
46: (ns/day) (hour/ns)
46: Performance: 96.620 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (291 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.346 0.174 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.456 2.838
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.7
46: (ns/day) (hour/ns)
46: Performance: 92.984 0.258
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (336 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.340 0.170 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.626 2.782
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.7
46: (ns/day) (hour/ns)
46: Performance: 92.236 0.260
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (333 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.339 0.170 199.3
46: (ns/day) (hour/ns)
46: Performance: 8.638 2.778
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 194.9
46: (ns/day) (hour/ns)
46: Performance: 92.870 0.258
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (333 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.339 0.170 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.634 2.780
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.6
46: (ns/day) (hour/ns)
46: Performance: 93.544 0.257
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (333 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.357 0.179 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.212 2.923
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.9
46: (ns/day) (hour/ns)
46: Performance: 93.633 0.256
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (341 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.341 0.171 199.3
46: (ns/day) (hour/ns)
46: Performance: 8.591 2.794
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.016 195.9
46: (ns/day) (hour/ns)
46: Performance: 94.349 0.254
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (333 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.342 0.172 199.4
46: (ns/day) (hour/ns)
46: Performance: 8.560 2.804
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.016 195.9
46: (ns/day) (hour/ns)
46: Performance: 94.596 0.254
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (333 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.391 0.196 199.4
46: (ns/day) (hour/ns)
46: Performance: 7.488 3.205
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.4
46: (ns/day) (hour/ns)
46: Performance: 93.605 0.256
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (358 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.291 0.146 199.2
46: (ns/day) (hour/ns)
46: Performance: 10.040 2.391
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.9
46: (ns/day) (hour/ns)
46: Performance: 93.799 0.256
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (309 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.325 0.163 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.022 2.660
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.031 0.016 195.3
46: (ns/day) (hour/ns)
46: Performance: 91.440 0.262
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (325 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.788 0.395 199.7
46: (ns/day) (hour/ns)
46: Performance: 3.722 6.448
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.8
46: (ns/day) (hour/ns)
46: Performance: 96.238 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (557 ms)
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (10740 ms total)
46:
46: [----------] 2 tests from Angles1/SimpleMdrunTest
46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Excluding 3 bonded neighbours molecule type 'butane'
46:
46: NOTE 2 [file angles1.top, line 72]:
46: In moleculetype 'butane' 4 atoms are not bound by a potential or
46: constraint to any other atom in the same moleculetype. Although
46: technically this might not cause issues in a simulation, this often means
46: that the user forgot to add a bond/potential/constraint or put multiple
46: molecules in the same moleculetype definition by mistake. Run with -v to
46: get information for each atom.
46:
46: Number of degrees of freedom in T-Coupling group System is 9.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 238.919 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'This_incredible_box_of_butane'
46: 50 steps, 0.1 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.277 0.139 199.6
46: (ns/day) (hour/ns)
46: Performance: 31.710 0.757
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (172 ms)
46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Excluding 3 bonded neighbours molecule type 'butane'
46:
46: NOTE 2 [file angles1.top, line 72]:
46: In moleculetype 'butane' 4 atoms are not bound by a potential or
46: constraint to any other atom in the same moleculetype. Although
46: technically this might not cause issues in a simulation, this often means
46: that the user forgot to add a bond/potential/constraint or put multiple
46: molecules in the same moleculetype definition by mistake. Run with -v to
46: get information for each atom.
46:
46: Number of degrees of freedom in T-Coupling group System is 9.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 238.919 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'This_incredible_box_of_butane'
46: 50 steps, 0.1 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.299 0.150 199.7
46: (ns/day) (hour/ns)
46: Performance: 29.442 0.815
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (183 ms)
46: [----------] 2 tests from Angles1/SimpleMdrunTest (357 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 65 tests from 7 test cases ran. (45178 ms total)
46: [ PASSED ] 65 tests.
46/54 Test #46: MdrunNonIntegratorTests ............. Passed 45.25 sec
test 47
Start 47: MdrunTpiTests
47: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml"
47: Test timeout computed to be: 600
47: [==========] Running 2 tests from 1 test case.
47: [----------] Global test environment set-up.
47: [----------] 2 tests from Simple/TpiTest
47: [ RUN ] Simple/TpiTest.ReproducesOutput/0
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1268 ms)
47: [ RUN ] Simple/TpiTest.ReproducesOutput/1
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (2750 ms)
47: [----------] 2 tests from Simple/TpiTest (4018 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 2 tests from 1 test case ran. (4018 ms total)
47: [ PASSED ] 2 tests.
47/54 Test #47: MdrunTpiTests ....................... Passed 4.04 sec
test 48
Start 48: MdrunMpiTests
48: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
48: Test timeout computed to be: 600
48: [==========] Running 22 tests from 7 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from DomainDecompositionSpecialCasesTest
48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -270835718
48: Generated 3 of the 3 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 3 of the 3 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 9.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.004 0.001 258.3
48: (ns/day) (hour/ns)
48: Performance: 59.291 0.405
48: This run will generate roughly 0 Mb of data
48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (47 ms)
48: [----------] 1 test from DomainDecompositionSpecialCasesTest (47 ms total)
48:
48: [----------] 4 tests from MimicTest
48: [ RUN ] MimicTest.OneQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -16394
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 362.3
48: (ns/day) (hour/ns)
48: Performance: 58.877 0.408
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.OneQuantumMol (28 ms)
48: [ RUN ] MimicTest.AllQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -142618625
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.002 359.8
48: (ns/day) (hour/ns)
48: Performance: 57.285 0.419
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.AllQuantumMol (27 ms)
48: [ RUN ] MimicTest.TwoQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -570920973
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.006 0.002 360.6
48: (ns/day) (hour/ns)
48: Performance: 56.289 0.426
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.TwoQuantumMol (27 ms)
48: [ RUN ] MimicTest.BondCuts
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -218112267
48: Generated 2211 of the 2211 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2211 of the 2211 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
48: Number of degrees of freedom in T-Coupling group rest is 66.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: NVE simulation: will use the initial temperature of 300.368 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
48:
48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.009 0.002 372.0
48: (ns/day) (hour/ns)
48: Performance: 37.700 0.637
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.BondCuts (79 ms)
48: [----------] 4 tests from MimicTest (161 ms total)
48:
48: [----------] 1 test from MultiSimTerminationTest
48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from MultiSimTerminationTest (0 ms total)
48:
48: [----------] 3 tests from PmeTest
48: [ RUN ] PmeTest.ReproducesEnergies
48: Setting the LD random seed to 2000972525
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.765 0.192 399.2
48: (ns/day) (hour/ns)
48: Performance: 9.470 2.534
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.523 0.131 398.8
48: (ns/day) (hour/ns)
48: Performance: 13.841 1.734
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.557 0.140 398.9
48: (ns/day) (hour/ns)
48: Performance: 12.990 1.848
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (570 ms)
48: [ RUN ] PmeTest.ScalesTheBox
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -1384383634
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.011 0.003 350.5
48: (ns/day) (hour/ns)
48: Performance: 28.842 0.832
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBox (40 ms)
48: [ RUN ] PmeTest.ScalesTheBoxWithWalls
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 1868906495
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Searching the wall atom type(s)
48: Number of degrees of freedom in T-Coupling group rest is 13.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: NVE simulation: will use the initial temperature of 966.268 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.038 0.010 380.0
48: (ns/day) (hour/ns)
48: Performance: 8.672 2.768
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBoxWithWalls (77 ms)
48: [----------] 3 tests from PmeTest (687 ms total)
48:
48: [----------] 1 test from ReplicaExchangeTerminationTest
48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
48:
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -4.79910463671071e+01
48: Maximum force = 1.86297359432218e+02 on atom 13
48: Norm of force = 8.77219865482161e+01
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2660 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 3.02331e+02 on atom 3
48: F-Norm = 1.18024e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -5.58622538633290e+01
48: Maximum force = 4.27274822366538e+02 on atom 13
48: Norm of force = 1.84530029253833e+02
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2606 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.19376899751521e+02
48: Maximum force = 9.99884921009767e+03 on atom 9
48: Norm of force = 4.61669565054298e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (463 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48:
48: NOTE 3 [file glycine_vacuo.top, line 12]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41575e+04 on atom 10
48: F-Norm = 1.18451e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.51743018140926e+02
48: Maximum force = 7.42089573409112e+03 on atom 9
48: Norm of force = 3.56929298615739e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (466 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.56984193848276e+02
48: Maximum force = 4.56923624626296e+02 on atom 17
48: Norm of force = 1.83258377168331e+02
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (81 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48:
48: NOTE 4 [file unknown]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 5 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 1.06800e+03 on atom 28
48: F-Norm = 4.26922e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.69410778678185e+02
48: Maximum force = 2.18225948474048e+02 on atom 17
48: Norm of force = 7.92068036537643e+01
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (84 ms)
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (6360 ms total)
48:
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents converged to Fmax < 10 in 1 steps
48: Potential Energy = -9.74257075835450e-01
48: Maximum force = 4.01322929015108e+00 on atom 3
48: Norm of force = 1.63839399694368e+00
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (29 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 4.01323e+00 on atom 3
48: F-Norm = 1.63839e+00
48:
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
48: Potential Energy = -9.90642313893957e-01
48: Maximum force = 2.57812909491105e+00 on atom 3
48: Norm of force = 1.05251679559258e+00
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (29 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (13 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.19395484891518e+02
48: Maximum force = 9.97041707197910e+03 on atom 9
48: Norm of force = 4.62274878665467e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (469 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41672e+04 on atom 10
48: F-Norm = 1.19357e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.56258793899479e+02
48: Maximum force = 7.50181017480397e+03 on atom 9
48: Norm of force = 3.61390332564874e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (470 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (450 ms)
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1460 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 22 tests from 7 test cases ran. (8715 ms total)
48: [ PASSED ] 22 tests.
48:
48: YOU HAVE 4 DISABLED TESTS
48:
48/54 Test #48: MdrunMpiTests ....................... Passed 8.75 sec
test 49
Start 49: MdrunMpiCoordinationTestsOneRank
49: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
49: Test timeout computed to be: 960
49: [==========] Running 27 tests from 3 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest
49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.220 0.221 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.656 3.606
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.121 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.143 1.976
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.107 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.670 1.756
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.116 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.675 1.894
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.506 1.654
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.410 1.666
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (934 ms)
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (934 ms total)
49:
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.678 1.635
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.121 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.119 1.980
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.116 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.667 1.895
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.099 0.099 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.814 1.620
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.102 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.458 1.660
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.345 1.798
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (792 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.696 1.633
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.113 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.021 1.843
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.820 1.872
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.106 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.807 1.738
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.394 0.394 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.727 6.440
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.251 0.252 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.833 4.114
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1250 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.828 2.029
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.129 0.129 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.388 2.107
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.6
49: (ns/day) (hour/ns)
49: Performance: 12.831 1.870
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.122 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.001 2.000
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.462 1.783
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.109 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.522 1.775
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (859 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.099 0.099 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.860 1.615
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.131 0.131 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.225 2.138
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.106 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.795 1.740
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.099 0.099 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.776 1.624
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.209 0.210 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.008 3.425
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.336 0.336 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.371 5.491
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1127 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.564 0.565 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.601 9.228
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.291 0.291 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.049 4.754
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.217 0.217 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.764 3.548
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.384 0.384 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.822 6.280
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.300 0.300 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.894 4.904
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.284 0.285 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.161 4.650
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2229 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.367 0.367 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.003 5.996
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.391 0.392 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.750 6.400
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.409 0.410 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.584 6.696
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.224 0.224 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.555 3.661
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.260 0.260 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.650 4.248
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.281 0.282 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.214 4.603
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2133 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.274 0.275 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.347 4.489
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.113 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.046 1.840
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.835 1.870
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.107 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.742 1.747
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.152 0.152 99.7
49: (ns/day) (hour/ns)
49: Performance: 9.669 2.482
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.386 1.793
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1016 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.582 1.907
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.086 1.986
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.886 2.019
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.107 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.776 1.742
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.412 1.789
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.423 1.788
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (834 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.656 1.757
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.121 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.116 1.981
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.122 0.123 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.959 2.007
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.836 1.870
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.610 1.643
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.476 1.781
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (825 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.107 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.688 1.753
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.104 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.044 1.709
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.622 1.762
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.813 2.032
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.126 0.127 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.586 2.071
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.119 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.383 1.938
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (833 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.601 1.905
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.113 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.016 1.844
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.107 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.763 1.744
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.107 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.775 1.742
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.411 1.790
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.500 1.655
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (800 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.183 0.183 99.8
49: (ns/day) (hour/ns)
49: Performance: 8.010 2.996
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.120 1.829
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.106 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.793 1.740
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.131 0.132 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.148 2.153
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.134 0.134 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.936 2.194
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.538 1.651
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (917 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.547 1.913
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.138 0.139 99.9
49: (ns/day) (hour/ns)
49: Performance: 10.593 2.266
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.658 1.637
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.674 1.636
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.340 1.674
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.128 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.477 2.091
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (824 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.133 0.133 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.007 2.180
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.084 1.986
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.729 1.885
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.107 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.715 1.750
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.364 1.796
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.374 1.794
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (842 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.439 1.786
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.113 0.114 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.924 1.857
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.117 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.589 1.906
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.582 1.907
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.301 1.678
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.292 1.679
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (799 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.529 1.774
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.138 0.138 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.644 2.255
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.123 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.894 2.018
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.750 1.882
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.409 1.790
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.455 1.927
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (859 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.717 1.631
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.096 0.097 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.212 1.578
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.099 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.748 1.627
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.610 1.763
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.268 1.809
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.406 1.666
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (758 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.142 0.142 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.326 2.324
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.113 0.113 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.998 1.846
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.768 1.880
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.107 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.778 1.742
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.458 1.783
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.126 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.688 2.053
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (859 ms)
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (18557 ms total)
49:
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.144 0.144 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.182 2.357
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.161 0.161 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.105 2.636
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.323 0.324 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.539 5.288
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.129 0.129 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.395 2.106
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.149 0.150 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.822 2.443
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.121 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.164 1.973
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (16239 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.122 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.023 1.996
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.248 1.812
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.102 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.445 1.661
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.096 0.096 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.222 1.577
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.273 0.274 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.365 4.473
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.133 0.134 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.979 2.186
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (16023 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.136 0.136 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.779 2.227
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.122 0.123 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.989 2.002
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.331 1.800
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.125 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.792 2.035
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.365 1.796
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.131 0.132 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.145 2.153
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (16014 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.294 0.294 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.996 4.804
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.078 1.987
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.137 0.137 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.713 2.240
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.571 1.909
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.127 0.128 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.488 2.089
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.133 0.133 99.6
49: (ns/day) (hour/ns)
49: Performance: 11.025 2.177
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (16258 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.220 0.220 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.664 3.601
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.193 0.193 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.594 3.160
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.144 0.144 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.202 2.352
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.126 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.675 2.056
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.131 0.132 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.150 2.152
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.113 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.043 1.840
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (16229 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.127 0.127 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.542 2.079
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.150 0.150 99.7
49: (ns/day) (hour/ns)
49: Performance: 9.776 2.455
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.159 0.159 99.7
49: (ns/day) (hour/ns)
49: Performance: 9.228 2.601
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.186 0.187 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.869 3.050
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.152 0.152 99.7
49: (ns/day) (hour/ns)
49: Performance: 9.656 2.485
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.139 0.140 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.506 2.284
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (16115 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.130 0.131 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.239 2.135
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.120 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.232 1.962
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.798 2.034
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.360 0.361 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.073 5.893
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.139 0.139 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.546 2.276
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.148 0.148 99.9
49: (ns/day) (hour/ns)
49: Performance: 9.921 2.419
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (16197 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.818 2.031
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.134 0.135 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.914 2.199
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.138 0.138 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.657 2.252
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.192 0.192 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.634 3.144
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.137 0.137 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.696 2.244
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.150 0.150 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.764 2.458
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (16140 ms)
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (129215 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 27 tests from 3 test cases ran. (148706 ms total)
49: [ PASSED ] 27 tests.
49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 148.74 sec
test 50
Start 50: MdrunMpiCoordinationTestsTwoRanks
50: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
50: Test timeout computed to be: 960
50: [==========] Running 27 tests from 3 test cases.
50: [----------] Global test environment set-up.
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest
50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.284 0.142 199.3
50: (ns/day) (hour/ns)
50: Performance: 10.317 2.326
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.250 0.126 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.696 2.052
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.257 0.129 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.392 2.107
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.277 0.139 198.7
50: (ns/day) (hour/ns)
50: Performance: 10.555 2.274
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.298 0.150 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.821 2.444
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.281 0.141 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.405 2.307
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1015 ms)
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1015 ms total)
50:
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.495 0.248 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.925 4.051
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.876 0.439 199.8
50: (ns/day) (hour/ns)
50: Performance: 3.349 7.167
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.918 0.460 199.8
50: (ns/day) (hour/ns)
50: Performance: 3.195 7.512
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.676 0.338 199.7
50: (ns/day) (hour/ns)
50: Performance: 4.341 5.529
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.715 0.358 199.7
50: (ns/day) (hour/ns)
50: Performance: 4.101 5.852
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.651 0.326 199.7
50: (ns/day) (hour/ns)
50: Performance: 4.504 5.329
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2333 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.762 0.382 199.7
50: (ns/day) (hour/ns)
50: Performance: 3.849 6.235
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.936 2.195
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.236 0.119 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.389 1.937
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.288 0.145 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.161 2.362
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.278 0.139 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.533 2.278
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.278 0.139 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.531 2.279
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1225 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.314 0.158 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.315 2.576
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.279 0.140 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.476 2.291
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.797 2.223
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.355 0.178 199.3
50: (ns/day) (hour/ns)
50: Performance: 8.251 2.909
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.297 0.149 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.859 2.434
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.268 0.135 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.910 2.200
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1066 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.193 2.144
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.311 0.156 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.410 2.551
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.240 0.121 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.183 1.970
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.240 0.120 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.204 1.967
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.229 0.115 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.764 1.880
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.281 0.141 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.420 2.303
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (951 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.288 0.145 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.145 2.366
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.939 2.194
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.272 0.137 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.760 2.230
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.222 0.112 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.165 1.823
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.264 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.083 2.165
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.288 0.145 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.163 2.361
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (973 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.277 0.139 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.544 2.276
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.495 0.248 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.922 4.053
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.221 0.111 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.195 1.819
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.238 0.119 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.292 1.952
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.277 0.139 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.554 2.274
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.244 0.123 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.960 2.007
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1050 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.209 0.105 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.968 1.718
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.201 0.101 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.536 1.651
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.189 0.095 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.415 1.557
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.191 0.096 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.288 1.570
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.211 0.106 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.841 1.734
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.229 0.115 198.8
50: (ns/day) (hour/ns)
50: Performance: 12.728 1.886
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (783 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.070 0.535 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.743 8.749
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.335 0.168 199.3
50: (ns/day) (hour/ns)
50: Performance: 8.729 2.749
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.222 0.112 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.136 1.827
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.256 0.128 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.433 2.099
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.278 0.140 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.528 2.280
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.277 0.139 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.562 2.272
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1391 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.342 0.171 199.3
50: (ns/day) (hour/ns)
50: Performance: 8.573 2.799
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.333 0.167 199.3
50: (ns/day) (hour/ns)
50: Performance: 8.785 2.732
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.221 0.111 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.223 1.815
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.338 0.170 199.3
50: (ns/day) (hour/ns)
50: Performance: 8.660 2.771
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.293 0.147 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.991 2.402
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.238 0.120 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.256 1.958
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1056 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.248 0.124 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.809 2.032
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.251 0.126 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.648 2.060
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.771 2.228
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.256 0.129 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.424 2.101
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.191 2.145
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.115 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.809 1.874
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (927 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.226 0.114 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.929 1.856
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.266 0.134 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.982 2.185
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.773 2.228
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.781 2.226
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.262 0.132 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.167 2.149
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.198 2.143
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (950 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.275 0.138 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.637 2.256
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.266 0.134 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.991 2.184
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.127 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.531 2.081
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.272 0.137 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.753 2.232
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.273 0.137 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.693 2.244
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.277 0.139 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.543 2.276
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (984 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.894 0.448 199.6
50: (ns/day) (hour/ns)
50: Performance: 3.279 7.319
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.934 0.467 199.7
50: (ns/day) (hour/ns)
50: Performance: 3.143 7.637
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.258 0.129 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.353 2.114
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.226 0.114 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.916 1.858
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.095 0.548 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.681 8.953
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.265 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.024 2.177
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1999 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.277 0.139 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.567 2.271
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.0
50: (ns/day) (hour/ns)
50: Performance: 10.960 2.190
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.272 0.137 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.735 2.236
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.256 0.129 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.428 2.100
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.260 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.225 2.138
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.329 0.165 199.2
50: (ns/day) (hour/ns)
50: Performance: 8.908 2.694
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1000 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.264 0.133 198.9
50: (ns/day) (hour/ns)
50: Performance: 11.070 2.168
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.262 0.132 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.156 2.151
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.488 0.245 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.004 3.998
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.648 0.325 199.5
50: (ns/day) (hour/ns)
50: Performance: 4.525 5.304
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.255 0.128 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.473 2.092
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.545 0.273 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.382 4.459
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1396 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.749 0.375 199.7
50: (ns/day) (hour/ns)
50: Performance: 3.915 6.131
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.571 0.286 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.133 4.675
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.538 0.270 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.448 4.405
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.739 0.870 199.9
50: (ns/day) (hour/ns)
50: Performance: 1.688 14.220
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.690 0.346 199.6
50: (ns/day) (hour/ns)
50: Performance: 4.249 5.648
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.483 0.242 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.069 3.955
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (2556 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.688 0.345 199.7
50: (ns/day) (hour/ns)
50: Performance: 4.261 5.632
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.685 0.343 199.7
50: (ns/day) (hour/ns)
50: Performance: 4.284 5.603
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.658 0.330 199.6
50: (ns/day) (hour/ns)
50: Performance: 4.457 5.385
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.408 0.205 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.175 3.345
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.211 0.106 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.832 1.735
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.343 0.172 199.3
50: (ns/day) (hour/ns)
50: Performance: 8.546 2.808
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1664 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.293 0.147 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.994 2.401
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.249 0.125 198.9
50: (ns/day) (hour/ns)
50: Performance: 11.747 2.043
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.221 0.111 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.225 1.815
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.238 0.119 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.293 1.952
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.938 2.010
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.294 0.148 199.1
50: (ns/day) (hour/ns)
50: Performance: 9.943 2.414
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (942 ms)
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (23248 ms total)
50:
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.352 0.176 199.4
50: (ns/day) (hour/ns)
50: Performance: 8.325 2.883
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.232 0.117 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.600 1.905
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.221 0.111 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.241 1.813
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.299 0.150 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.774 2.455
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.937 2.011
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.255 0.128 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.463 2.094
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (16040 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.791 2.224
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.238 0.120 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.258 1.958
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.268 0.135 199.0
50: (ns/day) (hour/ns)
50: Performance: 10.915 2.199
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.240 0.121 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.170 1.972
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.0
50: (ns/day) (hour/ns)
50: Performance: 10.958 2.190
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.215 0.108 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.583 1.767
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (16007 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.280 0.140 199.3
50: (ns/day) (hour/ns)
50: Performance: 10.469 2.292
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.259 0.130 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.305 2.123
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.251 0.126 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.653 2.060
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.221 1.964
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.218 0.110 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.399 1.791
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.277 0.139 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.546 2.276
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (15971 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.262 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.177 2.147
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.299 0.150 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.781 2.454
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.807 2.221
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.308 0.155 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.496 2.527
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.492 0.247 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.958 4.029
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.115 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.817 1.872
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (16174 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.216 1.965
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.242 0.121 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.099 1.984
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.250 0.126 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.698 2.052
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.264 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.079 2.166
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.260 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.250 2.133
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.258 0.129 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.355 2.114
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (15997 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.256 0.129 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.407 2.104
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.281 0.141 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.406 2.306
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.209 2.141
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.302 0.152 199.2
50: (ns/day) (hour/ns)
50: Performance: 9.678 2.480
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.220 1.964
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.250 0.126 198.9
50: (ns/day) (hour/ns)
50: Performance: 11.685 2.054
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (16040 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.264 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.081 2.166
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.257 0.129 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.383 2.108
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.274 0.138 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.655 2.252
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.240 0.121 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.184 1.970
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.262 0.132 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.151 2.152
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.260 0.130 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.256 2.132
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (16047 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.264 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.085 2.165
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.268 0.135 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.898 2.202
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.268 0.135 199.0
50: (ns/day) (hour/ns)
50: Performance: 10.902 2.201
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.252 0.127 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.610 2.067
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.256 0.129 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.429 2.100
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.244 0.123 198.9
50: (ns/day) (hour/ns)
50: Performance: 11.989 2.002
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (16023 ms)
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (128299 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 27 tests from 3 test cases ran. (152562 ms total)
50: [ PASSED ] 27 tests.
50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 152.59 sec
test 51
Start 51: GmxapiExternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 9 tests from 2 test cases.
51: [----------] Global test environment set-up.
51: [----------] 8 tests from GmxApiTest
51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
51: Setting the LD random seed to -50340127
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.281 0.141 199.5
51: (ns/day) (hour/ns)
51: Performance: 3.594 6.678
51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1228 ms)
51: [ RUN ] GmxApiTest.SystemConstruction
51: Setting the LD random seed to -11671810
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.SystemConstruction (2514 ms)
51: [ RUN ] GmxApiTest.SaneVersionComparisons
51: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
51: [ RUN ] GmxApiTest.VersionNamed0_1_Features
51: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
51: [ RUN ] GmxApiTest.RunnerBasicMD
51: Setting the LD random seed to 1875902397
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.277 0.139 199.5
51: (ns/day) (hour/ns)
51: Performance: 3.640 6.593
51: [ OK ] GmxApiTest.RunnerBasicMD (2660 ms)
51: [ RUN ] GmxApiTest.RunnerReinitialize
51: Setting the LD random seed to 1061121990
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51:
51: Received the remote INT/TERM signal, stopping within 50 steps
51:
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.247 0.124 199.3
51: (ns/day) (hour/ns)
51: Performance: 28.612 0.839
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.258 0.129 199.3
51: (ns/day) (hour/ns)
51: Performance: 27.386 0.876
51: [ OK ] GmxApiTest.RunnerReinitialize (2783 ms)
51: [ RUN ] GmxApiTest.RunnerContinuedMD
51: Setting the LD random seed to -520570883
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 10 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.268 0.134 199.4
51: (ns/day) (hour/ns)
51: Performance: 13.810 1.738
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.242 0.121 199.3
51: (ns/day) (hour/ns)
51: Performance: 29.228 0.821
51: [ OK ] GmxApiTest.RunnerContinuedMD (2783 ms)
51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
51: Setting the LD random seed to -1080692737
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 1 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.294 0.147 199.5
51: (ns/day) (hour/ns)
51: Performance: 2.289 10.487
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.225 0.113 199.3
51: (ns/day) (hour/ns)
51: Performance: 2.989 8.029
51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (2782 ms)
51: [----------] 8 tests from GmxApiTest (14750 ms total)
51:
51: [----------] 1 test from GmxApiBasicTest
51: [ RUN ] GmxApiBasicTest.Status
51: [ OK ] GmxApiBasicTest.Status (0 ms)
51: [----------] 1 test from GmxApiBasicTest (0 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 9 tests from 2 test cases ran. (14751 ms total)
51: [ PASSED ] 9 tests.
51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 14.78 sec
test 52
Start 52: GmxapiMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 9 tests from 2 test cases.
52: [----------] Global test environment set-up.
52: [----------] 8 tests from GmxApiTest
52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
52: Setting the LD random seed to -117967361
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.275 0.138 199.5
52: (ns/day) (hour/ns)
52: Performance: 3.675 6.530
52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1238 ms)
52: [ RUN ] GmxApiTest.SystemConstruction
52: Setting the LD random seed to -100936207
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.SystemConstruction (2532 ms)
52: [ RUN ] GmxApiTest.SaneVersionComparisons
52: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
52: [ RUN ] GmxApiTest.VersionNamed0_1_Features
52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
52: [ RUN ] GmxApiTest.RunnerBasicMD
52: Setting the LD random seed to 2146926525
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.291 0.146 199.5
52: (ns/day) (hour/ns)
52: Performance: 3.477 6.903
52: [ OK ] GmxApiTest.RunnerBasicMD (2682 ms)
52: [ RUN ] GmxApiTest.RunnerReinitialize
52: Setting the LD random seed to -4508434
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52:
52: Received the remote INT/TERM signal, stopping within 50 steps
52:
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.254 0.127 199.3
52: (ns/day) (hour/ns)
52: Performance: 27.828 0.862
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.258 0.129 199.3
52: (ns/day) (hour/ns)
52: Performance: 27.414 0.875
52: [ OK ] GmxApiTest.RunnerReinitialize (2808 ms)
52: [ RUN ] GmxApiTest.RunnerContinuedMD
52: Setting the LD random seed to 1052180474
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 10 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.280 0.140 199.4
52: (ns/day) (hour/ns)
52: Performance: 13.226 1.815
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.291 0.146 199.4
52: (ns/day) (hour/ns)
52: Performance: 24.285 0.988
52: [ OK ] GmxApiTest.RunnerContinuedMD (2841 ms)
52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
52: Setting the LD random seed to -68157442
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 1 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.265 0.133 199.5
52: (ns/day) (hour/ns)
52: Performance: 2.544 9.435
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.5-Raspbian-2020.5-4 (double precision)
52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.275 0.138 199.5
52: (ns/day) (hour/ns)
52: Performance: 2.450 9.798
52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (2815 ms)
52: [----------] 8 tests from GmxApiTest (14919 ms total)
52:
52: [----------] 1 test from GmxApiBasicTest
52: [ RUN ] GmxApiBasicTest.Status
52: [ OK ] GmxApiBasicTest.Status (0 ms)
52: [----------] 1 test from GmxApiBasicTest (0 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 9 tests from 2 test cases ran. (14919 ms total)
52: [ PASSED ] 9 tests.
52/54 Test #52: GmxapiMpiTests ...................... Passed 14.95 sec
test 53
Start 53: GmxapiInternalInterfaceTests
53: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 2 tests from 1 test case.
53: [----------] Global test environment set-up.
53: [----------] 2 tests from GmxApiTest
53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
53: Setting the LD random seed to -90391809
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (1025 ms)
53: [ RUN ] GmxApiTest.CreateApiWorkflow
53: Setting the LD random seed to -17082953
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.CreateApiWorkflow (1057 ms)
53: [----------] 2 tests from GmxApiTest (2082 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 2 tests from 1 test case ran. (2082 ms total)
53: [ PASSED ] 2 tests.
53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 2.11 sec
test 54
Start 54: GmxapiInternalsMpiTests
54: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalsMpiTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 2 tests from 1 test case.
54: [----------] Global test environment set-up.
54: [----------] 2 tests from GmxApiTest
54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
54: Setting the LD random seed to -269096205
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (1027 ms)
54: [ RUN ] GmxApiTest.CreateApiWorkflow
54: Setting the LD random seed to -1682047106
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.CreateApiWorkflow (1046 ms)
54: [----------] 2 tests from GmxApiTest (2073 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 2 tests from 1 test case ran. (2073 ms total)
54: [ PASSED ] 2 tests.
54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 2.10 sec
100% tests passed, 0 tests failed out of 54
Label Time Summary:
GTest = 472.20 sec*proc (54 tests)
IntegrationTest = 142.98 sec*proc (12 tests)
MpiTest = 327.26 sec*proc (8 tests)
SlowTest = 301.33 sec*proc (2 tests)
UnitTest = 27.89 sec*proc (40 tests)
Total Test time (real) = 472.30 sec
touch build-basic
dh_testdir
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 1%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 1%] Built target scanner
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/programs /<<PKGBUILDDIR>>/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 5%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 8%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2293 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
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/usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/mdrun_mpi.mpich ../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
Scanning dependencies of target scanner
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target lmfit_objlib
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target scanner
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/programs /<<PKGBUILDDIR>>/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In static member function 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = void; _Functor = gmx::FreeEnergyPerturbationElement::scheduleTask(gmx::Step, gmx::Time, const RegisterRunFunctionPtr&)::<lambda()>; _ArgTypes = {}]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:68:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
68 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::_ZN3gmx19StatePropagatorData24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 5%] Built target tng_io_obj
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 8%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const MPI_Comm*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
259 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
263 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
267 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2293 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/10/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:400:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
400 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
708 | lincs_update_atoms(lincsd, th, 1.0, sol, r,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
709 | (econq != ConstraintVariable::Force) ? invmass : nullptr, fp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1079:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1079 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1141:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1141 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1590 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1601:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1601 | stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1602 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1613:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1613 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1634:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1634 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1771:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1771 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1790:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1790 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
56 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:143:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
144 | state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::Update*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1752:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1752 | upd->deform()->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1868:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1868 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1896 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->sd()->randomize_group, upd->sd()->boltzfac);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function 'gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:338:26: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
338 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
741 | void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, int, double, const gmx::DensityFittingForceProviderState&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:79:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
79 | scaleToLattice({ &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:166:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
167 | { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:171:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:172:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
172 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:210:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
210 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:258:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
258 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:551:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:896:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
896 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1035:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1035 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1036 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
952 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:711:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
728 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
730 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
731 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
732 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
733 | &dvdlambda_lj, pmeFlags);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1004 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1384 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1393 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:379:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
379 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:421:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
421 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
422 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
424 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->